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-- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 9 Date: Fri, 26 Sep 2014 13:14:05 +0200 From: James Starlight <jmsstarlight.gmail.com> Subject: Re: [AMBER] bash scripting for MD tasks To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAALQopxgz84uJ2D7g598OFykvDFzcvVLzvV5sWUVBuHtBkbgAA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 The general idea here to avoid palatalization and just run jobs still being in loop using 2 variables one corresponded to the looping over GPUs iDs and the second to the folder of each simulation. Below you could find two examples (unfortunately both still incomplete because I'm not an expert in BASH) #!/bin/bash # set workdir with proteins dirr=/home/gleb/Documents/script simulations=/home/gleb/Documents/script/Simulations #run each simulation in parallel using nested loop which might not be good solution : here the problem that some condition should be provided to avoid using >1 simulation on the same GPU # i=0 # the number of first GPU which will be used! while i < n ; do # the maximum number of the available GPUs on the machines # m.b n also might be obtained using some command ? # !!!!some condition should be specified to pass sharing SAME GPU between different md runs !!! export CUDA_VISIBLE_DEVICES "$i" for sim in $simulations/* ; do simulation=$(basename "$sim") echo "Simulation of ${simulation} is in a progress on ${i} GPU!!" cd $sim chmod +x ./${simulation}.Sh ./${simulation}.Sh & echo "Simulation of ${simulation} has been finished" done done # alternatively possibility to do the same taks using 2 variables within one FOR loop-> here we must have the same number of the GPUs and MD jobs. for i in {0..$n}, sim in $simulations/* ; do # it seems that problem here in the syntax!!! export CUDA_VISIBLE_DEVICES "$i" simulation=$(basename "$sim") echo "Simulation of ${simulation} is in a progress on ${i} GPU!" cd $sim chmod +x ./${simulation}.Sh ./${simulation}.Sh & echo "Simulation of ${simulation} has been finished" done So I'll be very (very!!) thankful for possible suggestion regarding both cases Kind regards, James 2014-09-26 11:43 GMT+02:00 James Starlight <jmsstarlight.gmail.com>: > Dear all, > > I wounder to ask some suggestions about possibility to improve my launch > script aimed on the running of several similations. > > e.g my current protocol use simple looping over the dir with the > simulations to run sh file in each folder which is call for the pmemd etc > for each system > > #!/bin/bash > > # set workdir with proteins > dirr=/home/gleb/Documents/script > simulations=/home/gleb/Documents/script/Simulations > > > > #run each simulation > for sim in $simulations/* ; do > simulation=$(basename "$sim") > echo "Simulation of ${simulation} is in a progress!" > cd $sim > chmod +x ./${simulation}.Sh > ./${simulation}.Sh > echo "Simulation of ${simulation} has been finished" > done > > how this script can be improved to i) avoid call sh from the another sh? > ii) to run several jobs in parallel corresponded to the number of available > GPU of my workstation ? > > Thanks for help, > > James > ------------------------------ Message: 10 Date: Fri, 26 Sep 2014 12:31:26 +0000 From: Parker de Waal <Parker.deWaal.vai.org> Subject: Re: [AMBER] Combined cartesian and NMR restraints To: AMBER Mailing List <amber.ambermd.org> Message-ID: <974700F6B71AA04897B9105CC7E1AAFA7B3363.VAIEXMB01.vai.org> Content-Type: text/plain; charset="us-ascii" Another update - I've switched from CUDA 6.5 to 5.5, however the error remains the same: Error: unspecified launch failure launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed unspecified launch failure Is it possible that because both my cartesian restraints (only on chain A) AND NMR restraints (tethering chain B to chain A) affect some of the same residues that PMEMD.CUDA is crashing and that this combination is not possible? Best, Parker ________________________________________ From: Parker de Waal Sent: Thursday, September 25, 2014 11:26 PM To: AMBER Mailing List Subject: RE: [AMBER] Combined cartesian and NMR restraints Hi David, Thank you for the input. I've adjusted the input per your suggestion as follows: NVT prod &cntrl irest=1, ntx =5, nstlim=5000000, dt=0.002, ntpr=500, ntwr=500, ntwx=500, temp0=300.0, ntt=3, gamma_ln=5, ntb=1, ntp=0, ntc=2, ntf=2, ig=-1, cut=9, ioutfm = 1, iwrap=1, nmropt=1, ntr=1, restraint_wt=20., restraintmask=':1-708', / &wt type='END' / DISANG=rst.dist The only problem now is that when I run pmemd.CUDA the follow error occurs: Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered I'm currently using the most recent version of AMBER14 (updated and recompiled today) with NVIDIA Driver Version: 340.32 and Cuda compilation tools, release 6.5, V6.5.12 (I'm running arch so rolling back is difficult, but I'm trying now to 5.5) Parker ________________________________________ From: David A Case [case.biomaps.rutgers.edu] Sent: Thursday, September 25, 2014 10:56 PM To: AMBER Mailing List Subject: Re: [AMBER] Combined cartesian and NMR restraints On Fri, Sep 26, 2014, Parker de Waal wrote: > > After reading through some of the old mailing list threads regarding > the various workarounds for ntr =1 and nmropt=1, I still need some > clarification. > > I have an NVT http://scanmail.trustwave.com/?c=129&d=49Wk1K_bbQBiQ3IZT3Q0OKQyeRAK9WcrWuJ7VB2iCg&u=http%3a%2f%2fprod%2ein as show below: > > > Now I wish to add cartesian restraints, following the snippet here: > http://scanmail.trustwave.com/?c=129&d=49Wk1K_bbQBiQ3IZT3Q0OKQyeRAK9WcrWuUuUBb1CQ&u=http%3a%2f%2fambermd%2eorg%2fQuestions%2fconstraints%2ehtml into my rst.dist file as > seen below: The group cards for cartesian restraints go into the mdin file, not into the restraints file. > > # N373 D69 VS > &rst > ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7, > rk2=0.0, rk3=25.0, ir6=1, ialtd=0, > &end > ... (lines removed) > # A150 F244 VS > &rst > ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7, > &end > Hold GPCR fixed > 20.0 > RES 1 708 > END > END > > However whenever I run this the follow error occurs: > > 5. REFERENCE ATOM COORDINATES > > default_name > ----- READING GROUP 1; TITLE: > DISANG=rst.dist Note that the program thinks the DISANG card is the title for the cartesian restraints; so somehow it is not reading the NMR-like restraints correctly. The first thing you need to do is set ntr=0, and make sure that you are getting the NMR restraints correctly processed. Follow the example in the $AMBERHOME/test/nmr directory. By far the simplest thing to do for cartsian restraints is to set them in the cntrl namelist: ntr=1, restraint_wt=20., restraintmask=':1-708', Then there is no need for any GROUP input. Beyond this: You could try using the correct "/" rather than the obsolete (and never standard "&end" to end namelists. But that is probably not the source of the problem. You may need to let us know which program you are running (sander or pmemd?) and which version. Posting the entire mdout file is probably also required...there is something subtle that is preventing your file from being parsed correctly. ....dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://scanmail.trustwave.com/?c=129&d=5NWk1DkJ-rwIWc9WjII5xYe7GxkTZDMTXvE-6uITXQ&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2famber ------------------------------ Message: 11 Date: Fri, 26 Sep 2014 20:49:17 +0800 (GMT+08:00) From: ?? <shiw12.mails.tsinghua.edu.cn> Subject: [AMBER] Fw: Welcome to Beijing for the 15th International Congress of Quantum Chemistry To: amber <amber.ambermd.org> Message-ID: <512ee358.8cd3.148b20223c9.Coremail.shiw12.mails.tsinghua.edu.cn> Content-Type: text/plain; charset=UTF-8 Dear Colleagues, The 15th International Congress of Quantum Chemistry (ICQC) will take place in Beijing, June 8-13, 2015. The registration will be opened by Oct 1, 2014. Please browse http://www.icqc2015.org/. The following eminent theoretical chemists have accepted the invitation for lectures: Millard Alexander (U Maryland), Yuriko Aoki (Kyushu U), Paul Ayers (McMaster U), Joel Bowman (Emory U), Ria Broer-Braam (Groningen U), Filipp Furche (UC Irvine), Jiali Gao (U Minnesota), Yiqin Gao (Peking U), Stefan Grimme (U Bonn), Sharon Hammes-Schiffer (UIUC), Martin Head-Gordon (UC Berkeley), Dudley Herschbach (Harvard, Nobel Laureate), Roald Hoffmann (Cornell U, Nobel Laureate), Kendall Houk (UCLA), Denis Jacquemin (U Nantes), Poul J?rgensen (U Aarhus), Kwang S. Kim (Ulsan), Wanzhen Liang (Xiamen U), Carmay Lim (Acad Sinica), Yi Luo (KTH), Rudolf Marcus (Caltech, Nobel Laureate), Benedetta Mennucci (U Pisa), Josef Michl (U Colorado), Keiji Morokuma (U Kyoto), Hiroshi Nakatsuji (QCRI), Jozef Noga (Comenius U), Oleg Prezhdo (U So Calif), Leo Radom (U Sydney), Lucia Reining(Ecole Polytech), Andreas Savin (UPMC), George Schatz (Northwester U), H. Bernhard Schlegel (Wayne State U), Tamar Seideman (Northwestern U), Juha Vaara (U Oulu), Xin Xu (Fudan U), Yijing Yan (Hong Kong UST), Xueming Yang (DICP), Donghui Zhang (DICP) The registration fee is 350 EUROs (regular) and 175 EUROs (student), which covers (i) conference and reception, coffee breaks, all the lunches; (ii) tour to the Great Wall; (iii) refreshments in the four poster sessions. The conference venue will be in the Tsinghua University Campus (ranked by Forbes as one of the 14 most beautiful University Campuses in the world, only one from Asia), easy connected by subways and other public transport. Many hotels, restaurants, supermarkets, cafes are within the distance of 20-minute walk. You may also easily rent a bicycle for one week or even one month for less than 10 EUROs. Beijing is a fantastic place to see. And this is the very first ICQC in China. Please check the air quality of Beijing in http://aqicn.org/city/beijing/ : Beijing is not much worse than other megacities like Tokyo or New York on average. The air quality in the first half of June will be satisfactory and it is sure that you will enjoy the sunshine and the cosy temperature. There will be eight satellite meetings featuring on specialized directions of theoretical and computational chemistry. Please consult the website. Please mark your calendar. We look forward to welcoming you in China! Sincerely, Zhigang Shuai, Weihai Fang, Wenjian Liu, Weitao Yang Organizing Committee of the 15th ICQC http://www.icqc2015.org/ ------------------------------ Message: 12 Date: Fri, 26 Sep 2014 09:47:45 -0400 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] cpptraj/parmbox To: amber.ambermd.org Message-ID: <1411739265.29713.4.camel.gmail.com> Content-Type: text/plain; charset="UTF-8" On Fri, 2014-09-26 at 00:13 -0700, amirhossein taghavi wrote: > Hello everyone, > > My rpoblem is not directly related to MD but as I use Amber cpptraj to > analyze my data, I wondered may some one could have some help!! > > I have a CG model of DNA in xyz format and I am using cpptraj to do > some measurements on bonds,angles and dihedrals.The problem is, for > example, when I calculate the base interdistances with piece of a > script I have, in some frames the distance is calculated with the > image of particle at the end of the box, like say my box is 136A. so > if the usual BB distance is between 5-7A is some frames it jumps tp > 136. > I have added parmbox information to the script but the problem still > exists. > any help or suggestion is highly appreciated. By default, cpptraj uses the minimum image convention when computing distances (unless you use the keyword "noimage"). If you are getting wonky distances, perhaps your box is not correctly defined? Your cpptraj output should provide information about your files (like, for instance, any box information that may be present). Does it look right to you? HTH, Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 13 Date: Fri, 26 Sep 2014 07:59:59 -0600 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] cpptraj/parmbox To: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>, AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOaO6Gd94+uQL6kshM1LhOiSiuY0DAP8ymUY+XnkzutiZA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi, We need much more information on how the original trajectory was generated, as well as the full cpptraj output to even begin to diagnose this problem. -Dan On Fri, Sep 26, 2014 at 1:13 AM, amirhossein taghavi <amirhosseintaghavi240.yahoo.com> wrote: > Hello everyone, > > My rpoblem is not directly related to MD but as I use Amber cpptraj to analyze my data, I wondered may some one could have some help!! > > I have a CG model of DNA in xyz format and I am using cpptraj to do some measurements on bonds,angles and dihedrals.The problem is, for example, when I calculate the base interdistances with piece of a script I have, in some frames the distance is calculated with the image of particle at the end of the box, like say my box is 136A. so if the usual BB distance is between 5-7A is some frames it jumps tp 136. > I have added parmbox information to the script but the problem still exists. > any help or suggestion is highly appreciated. > > Thanks in Forward > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) ------------------------------ Message: 14 Date: Fri, 26 Sep 2014 10:05:01 -0400 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] Combined cartesian and NMR restraints To: amber.ambermd.org Message-ID: <1411740301.29713.6.camel.gmail.com> Content-Type: text/plain; charset="UTF-8" On Fri, 2014-09-26 at 12:31 +0000, Parker de Waal wrote: > Another update - I've switched from CUDA 6.5 to 5.5, however the error remains the same: > > Error: unspecified launch failure launching kernel kClearForces > cudaFree GpuBuffer::Deallocate failed unspecified launch failure > > Is it possible that because both my cartesian restraints (only on > chain A) AND NMR restraints (tethering chain B to chain A) affect some > of the same residues that PMEMD.CUDA is crashing and that this > combination is not possible? What happens if you turn off all of the restraints? Does it work? Does it work with the CPU? Here is a good workflow for debugging pmemd.cuda issues: 1. Run the pmemd.cuda test suite and make sure that the tests run, and the majority pass (and that the failures are small differences). (This should really be step 0, since hopefully you've already done this part.) 2. Does the pmemd.cuda simulation fail reliably? That is, do you get the EXACT same behavior every time? (i.e., it fails on the same step with the same error message, and yields identical energies each time if it gets that far?) 3a. If the answer to 2 is "no", download and run the GPU validation test suite. If that test fails, RMA your bad GPU and skip to step 6. If the test passes, continue to 3b or 4. 3b. Try reducing the feature set of your simulation to make sure "plain" molecular dynamics works. If "plain" MD works, try adding the "extras" separately until you find the minimal combination that fails. This will help narrow down where to look. 4. Run the problematic simulation using pmemd on the CPU. Does it fail? 5a. If it fails, have a look at the error message -- pmemd and pmemd.MPI are very often better at giving informative error messages than pmemd.cuda (which often just says the equivalent of "something went wrong"). 5b. If the CPU works, then the problem is more likely (although still not certainly) a problem with pmemd.cuda, so consult this list, giving as much detail as possible (including what you've done so far). 6. Have a beer. Or a glass of milk. Of course there are more things you can try -- like reducing ntpr and ntwx to very small numbers (e.g., 1) so that you can visualize what is happening each step leading up to the crash (you may have to run some MD to get your system "close" if it happens after thousands of steps). Hope this helps, Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 15 Date: Fri, 26 Sep 2014 17:21:04 +0200 From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com> Subject: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CACF5EqmCBhLNGjw978r50tFrxrT5rVrUVw7GX=j7NkpfsiQg3A.mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Amberists; I am running tleap using AMBER 12 with the following script on a receptor which is attached herewith. During running the Leap I am encountering this problem " FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type. Failed to generate parameters Parameter file was not saved. Writing pdb file: rec_solvated.pdb Converting N-terminal residue name to PDB format: NLEU -> LEU Converting C-terminal residue name to PDB format: CLEU -> LEU Quit " I would highly appreciate any response in this regard. Thank you for all your time. tleap.in source leaprc.ff99SB receptor = loadPDB rec.pdb saveAmberParm receptor rec.top rec.crd charge receptor addIons2 receptor Cl- 0 solvateBox receptor TIP3PBOX 8.0 saveAmberParm receptor rec_solvated.top rec_solvated.crd savepdb receptor rec_solvated.pdb quit -- Thanks & Regards; Soumendranath Bhakat Researcher Molecular Modelling and Drug Design Research Group Discipline of Pharmaceutical Sciences UKZN, Westville Weblink: http://soliman.ukzn.ac.za/Home.aspx Past: Department of Pharmaceutical Sciences Birla Institute of Technology, Mesra, India in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/ -------------- next part -------------- A non-text attachment was scrubbed... Name: rec_apo.pdb Type: chemical/x-pdb Size: 205514 bytes Desc: not available Url : http://lists.ambermd.org/mailman/private/amber/attachments/20140926/4f63c471/attachment-0001.pdb ------------------------------ Message: 16 Date: Fri, 26 Sep 2014 11:26:22 -0400 From: Carlos Simmerling <carlos.simmerling.gmail.com> Subject: Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAGk3s-QCFhE6dJNH=A=mxmLk08RCQDVBCXuJe7XQ_iKYqYeQ6A.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 if you look at your PDB file, you'll see that there are H atoms listed only for NLEU, not for any other residue. also, these H atoms all have the same name. Perhaps you might want to look into the source of this pdb file, and see if those H atoms really should be in your file or not. If so, you need to tell Amber which atom each of these H's are, since it doesnt' really have a way to figure it out if the names are all just "H". On Fri, Sep 26, 2014 at 11:21 AM, Soumendranath Bhakat < bhakatsoumendranath.gmail.com> wrote: > Dear Amberists; > > I am running tleap using AMBER 12 with the following script on a receptor > which is attached herewith. During running the Leap I am encountering this > problem > > " > FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type. > Failed to generate parameters > Parameter file was not saved. > Writing pdb file: rec_solvated.pdb > Converting N-terminal residue name to PDB format: NLEU -> LEU > Converting C-terminal residue name to PDB format: CLEU -> LEU > Quit > " > > I would highly appreciate any response in this regard. > Thank you for all your time. > > > tleap.in > > source leaprc.ff99SB > receptor = loadPDB rec.pdb > saveAmberParm receptor rec.top rec.crd > charge receptor > addIons2 receptor Cl- 0 > solvateBox receptor TIP3PBOX 8.0 > saveAmberParm receptor rec_solvated.top rec_solvated.crd > savepdb receptor rec_solvated.pdb > quit > > -- > Thanks & Regards; > Soumendranath Bhakat > Researcher > Molecular Modelling and Drug Design Research Group > Discipline of Pharmaceutical Sciences > UKZN, Westville > Weblink: http://soliman.ukzn.ac.za/Home.aspx > Past: Department of Pharmaceutical Sciences > Birla Institute of Technology, Mesra, India > in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/ > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > ------------------------------ Message: 17 Date: Fri, 26 Sep 2014 11:54:02 -0400 From: David A Case <case.biomaps.rutgers.edu> Subject: Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20140926155402.GB3761.biomaps.rutgers.edu> Content-Type: text/plain; charset=us-ascii On Fri, Sep 26, 2014, Soumendranath Bhakat wrote: > FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type. To expand/simplify what Carlos said: Your PDB file has a atom named "H" in the first resdidue. But the IUPAC/PDB/Amber nomenclature for an N-terminal amino acid does not have any such atoms: the three hydrogens bonded to the "N" atom are called H1, H2, and H3. So, the PDB atom names don't match the library atom names, and tleap doesn't know what to do, and quits. As Carlos said, the simplest thing to do is just to remove the "H" atom from the PDB file. Another option is to use the "reduce" program first. Even better would be to get in the habit of using "pdb4amber" before running tleap. ...dac ------------------------------ Message: 18 Date: Fri, 26 Sep 2014 08:57:15 -0700 From: Ross Walker <ross.rosswalker.co.uk> Subject: Re: [AMBER] bash scripting for MD tasks To: AMBER Mailing List <amber.ambermd.org> Message-ID: <D04AD9B9.49AC4%ross.rosswalker.co.uk> Content-Type: text/plain; charset="US-ASCII" Hi James, I haven't looked through the syntax here completely but one thing to note: On 9/26/14, 4:14 AM, "James Starlight" <jmsstarlight.gmail.com> wrote: >The general idea here to avoid palatalization and just run jobs still >being >in loop using 2 variables one corresponded to the looping over GPUs iDs >and >the second to the folder of each simulation. >Below you could find two examples (unfortunately both still incomplete >because I'm not an expert in BASH) > >#!/bin/bash > ># set workdir with proteins >dirr=/home/gleb/Documents/script >simulations=/home/gleb/Documents/script/Simulations > >#run each simulation in parallel using nested loop which might not be good >solution : here the problem that some condition should be provided to >avoid >using >1 simulation on the same GPU ># >i=0 # the number of first GPU which will be used! >while i < n ; do # the maximum number of the available GPUs on the >machines ># m.b n also might be obtained using some command ? > # !!!!some condition should be specified to pass sharing SAME GPU between >different md runs !!! > export CUDA_VISIBLE_DEVICES "$i" > for sim in $simulations/* ; do > simulation=$(basename "$sim") > echo "Simulation of ${simulation} is in a progress on ${i} GPU!!" > cd $sim > chmod +x ./${simulation}.Sh > ./${simulation}.Sh & ---> without a 'wait' here the echo line below will immediately be printed because you backgrounded the previous command. The better way to do this is to put the GPU loop as the inner loop and the simulations as the outer loop. And include a 'wait' after the done on the inner loop. This will work reasonably efficiently as long as the simulations take similar wall clock times. The alternative is to have an actual fork in your bash script - run it in multiple threads or using 'parallel' - I forget the syntax. Or alternatively run two completely separate bash scripts, or install a queuing system. Note if you set the GPUs to exclusive process mode (nvidia-smi -c 3) then you do not need to set CUDA_VISIBLE_DEVICES. pmemd.cuda will automatically select a free GPU. However this will disable multiGPU runs using peer to peer so you need to set it back to default (nvidia-smi -c 0) if you want to run pmemd.cuda.MPI. > echo "Simulation of ${simulation} has been finished" > done >done HTH, All the best Ross > ------------------------------ Message: 19 Date: Fri, 26 Sep 2014 11:21:42 -0600 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] cpptraj/parmbox To: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>, AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOb3tey5JLtNyggTZR8pMxHsc=Ej7kr0Zb0QToZRCyaG4A.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi, You've come across a corner case. The problem is that since the trajectory only contains box lengths (no angles), cpptraj by default checks the topology to determine what kind of box is present. However, since you are presumably using your PDB file as your topology (which has no box info), cpptraj doesn't know what kind of box it is. In the end the coordinates are read in fine, but the box information is not used because cpptraj doesn't assume the box is orthogonal. The 'parmbox' command can help, but since you only gave it lengths (not angles) it still has no idea what the box type is. Add 'alpha 90 beta 90 gamma 90' to the 'parmbox' command to set an orthogonal box. Hope this helps, -Dan On Fri, Sep 26, 2014 at 8:19 AM, amirhossein taghavi <amirhosseintaghavi240.yahoo.com> wrote: > Hi, > > The original trajectory file is the output of my MC code for GC DNA modeling > in the xyz format.I have two scripts which produce pdb and trj files which > based on that cpptraj analysis is done. > > This is a sample of cpptraj output: > > Reading '1.xyz.pdb' as PDB File > 1.xyz.pdb: determining bond info from distances. > Warning: 1.xyz.pdb: Determining default bond distances from element types. > INPUT: Reading Input from STDIN > [parmbox x 136.12 y 136.12 z 136.12] > [trajin 1.xyz.trj] > Reading '1.xyz.trj' as Amber Trajectory > [distance .82 .82 out distBB_41.dat geom noimage] > DISTANCE: .82 to .82, non-imaged, geometric center. > > I have attached the original trajectory file and trj,pdb files hope that it > helps.if the scripts that are used to get pdb and trj files are also needed > please let me know. > > Thanks in Forward > Amir > > > > > On Friday, September 26, 2014 4:00 PM, Daniel Roe <daniel.r.roe.gmail.com> > wrote: > > > Hi, > > We need much more information on how the original trajectory was > generated, as well as the full cpptraj output to even begin to > diagnose this problem. > > -Dan > > On Fri, Sep 26, 2014 at 1:13 AM, amirhossein taghavi > <amirhosseintaghavi240.yahoo.com> wrote: >> Hello everyone, >> >> My rpoblem is not directly related to MD but as I use Amber cpptraj to >> analyze my data, I wondered may some one could have some help!! >> >> I have a CG model of DNA in xyz format and I am using cpptraj to do some >> measurements on bonds,angles and dihedrals.The problem is, for example, when >> I calculate the base interdistances with piece of a script I have, in some >> frames the distance is calculated with the image of particle at the end of >> the box, like say my box is 136A. so if the usual BB distance is between >> 5-7A is some frames it jumps tp 136. >> I have added parmbox information to the script but the problem still >> exists. >> any help or suggestion is highly appreciated. >> >> Thanks in Forward > >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe, PhD > Department of Medicinal Chemistry > University of Utah > 30 South 2000 East, Room 307 > Salt Lake City, UT 84112-5820 > http://home.chpc.utah.edu/~cheatham/ > (801) 587-9652 > (801) 585-6208 (Fax) > -- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber End of AMBER Digest, Vol 989, Issue 1 ************************************* _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Sep 29 2014 - 01:00:02 PDT