Thanks for your replying.
I installed Xcode 11 to compile Amber. Maybe I should install an older vision of Xcode?
Thanks.
Hanlu Gao
> 2020年6月22日 上午3:00，amber-request.ambermd.org 写道：
>
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: error: installing amber18 on MacOS (Gustaf Olsson)
> 2. How to install Ambertools 20 using Cygwin and CMake on
> windows 7? (Ibrahim Mohamed)
> 3. Re: Incompatibility of coordinate file with topology after
> minimization (David A Case)
> 4. Re: Tutorials unavailable (Sruthi Sudhakar)
> 5. Re: Tutorials unavailable (Ahmed Elrashedy)
> 6. How to use Ambertools20 parmed.py? (Ibrahim Mohamed)
> 7. Re: Incompatibility of coordinate file with topology after
> minimization (Houcemeddine Othman)
> 8. Re: How to use Ambertools20 parmed.py? (David A Case)
> 9. Re: Tutorials unavailable (Rodrigo Galindo-Murillo)
> 10. pH-REMD error (Kolattukudy P. Santo)
> 11. Re: pH-REMD error (Cruzeiro,Vinicius Wilian D)
> 12. Re: pH-REMD error (Kolattukudy P. Santo)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 20 Jun 2020 21:19:07 +0000
> From: Gustaf Olsson <gustaf.olsson.lnu.se>
> Subject: Re: [AMBER] error: installing amber18 on MacOS
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <be47478837e24f45b8a61358151428fe.lnu.se>
> Content-Type: text/plain; charset="iso-8859-1"
>
> What version of Xcode do you have installed?
>
>
> I have still not found the time to update the current instructions for installing on OS X though the ld issue was a problem with previous installls as Apple dropped support for some libraries.
>
>
> // Gustaf
>
> ________________________________
> Fr?n: gaohanlu <gaohanlu95.163.com>
> Skickat: den 18 juni 2020 16:29:58
> Till: AMBER Mailing List
> ?mne: [AMBER] error: installing amber18 on MacOS
>
> Dear all,
> I tried to install amber18 on macOS 10.15. I have installed Xcode11 and command lines tools.
> When I compiled amber18 with macOS clang using the command line:
> ./configure -noX11 -macAccelerate clang
> I got the following error. Can somebody please help me?
> ld: library not found for -lmc
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> ./configure2: line 2643: ./testp: No such file or directory
> Error: Unable to compile mixed C/Fortran code.
> Please check your compiler settings and configure flags.
> Configure failed due to the errors above!
> Thanks
> Gao hanlu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 20 Jun 2020 21:32:32 +0000 (UTC)
> From: Ibrahim Mohamed <hollow_ichigo199799.yahoo.com>
> Subject: [AMBER] How to install Ambertools 20 using Cygwin and CMake
> on windows 7?
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <1107228885.2371903.1592688752260.mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Greetings sir,
> I want to install Ambertools 20 on windows 7 using CygWin and CMake. I tried it but it seems that it cant find the python libraries, however they can be imported in python normally.
> I have python (2.7.13), latest version of CMake and Cygwin.
>
> this is the error:
> -- Found PythonLibs: C:/Python27/Lib (found version "")C:\Python27\pythonw.exe: can't open file '/cygdrive/d/games/amber/AmberTools20/amber20_src/cmake/python_packagecheck.py': [Errno 2] No such file or directory-- Checking for Python package numpy -- not foundC:\Python27\pythonw.exe: can't open file '/cygdrive/d/games/amber/AmberTools20/amber20_src/cmake/python_packagecheck.py': [Errno 2] No such file or directory-- Checking for Python package scipy -- not foundC:\Python27\pythonw.exe: can't open file '/cygdrive/d/games/amber/AmberTools20/amber20_src/cmake/python_packagecheck.py': [Errno 2] No such file or directory-- Checking for Python package matplotlib -- not foundC:\Python27\pythonw.exe: can't open file '/cygdrive/d/games/amber/AmberTools20/amber20_src/cmake/python_packagecheck.py': [Errno 2] No such file or directory-- Checking for Python package setuptools -- not found
> This is what i have in run_cmake file (for linux):
> cmake $AMBER_PREFIX/amber20_src \? ? -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \? ? -DCOMPILER=GNU? \? ? -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \? ? -DDOWNLOAD_MINICONDA=FALSE -DMINICONDA_USE_PY3=TRUE \? ? -DPYTHON_EXECUTABLE="C:/Python27/pythonw.exe" \? ? -DPYTHON_INCLUDE_DIR="C:/Python27/include/" \? ? -DPYTHON_LIBRARY="C:/Python27/Lib"?
>
> Please tell me how can i install Ambertools 20.
> Thanks in advance.
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 20 Jun 2020 21:22:06 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Incompatibility of coordinate file with topology
> after minimization
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200621012206.wthak5otrslw6pcy.sasc8f750522ecc.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Sat, Jun 20, 2020, Houcemeddine Othman wrote:
>
>> I am running a restrained minimization step of a
>> protein+solvent+counterions system using the following input
>>
>> minimization parameters
>> &cntrl
>> imin = 1, maxcyc = 7000, ncyc = 1000, cut = 12, ntb = 1, ntr = 0, igb = 0,
>> drms = 0.01
>> /
>> sander -O -i energy_min1.in -o energy_min1.out -c sructure_start.rst7 -p
>> structure.prmtop -r structure_min1.rst7 -ref sructure_start.rst7
>>
>> Everything runs successfully. However, the resulting minimized structure
>> (structure_min1.rst7) contains lesser information (2 Mb) than the starting
>> structure (sructure_start.rst7, 3Mb). It is also not compatible with the
>> topology file (structure.prmtop).
>
> The default format for restart files is netcdf, which will often by
> smaller than a formatted form. Use the "file" command to see which
> files are formatted ("ASCII") and which are not ("data").
>
> [The ntxo variable controls the format of restart files; but we
> recommend sticking with the default unless you know you have a good
> reason not to.]
>
> How did you conclude that the min1 restart file is not compatible with
> the prmtop file?
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 21 Jun 2020 11:38:32 +0530
> From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
> Subject: Re: [AMBER] Tutorials unavailable
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAG8eZXw2rEKh1a_rU8N-5fsy3mu0OYc-LEHRwR0gYjUUsL6L8g.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you all for the response
>
> On Sun, Jun 21, 2020 at 12:17 AM Preeti Pandey <preetipandey2806.gmail.com>
> wrote:
>
>> For the time being, you can have a look at the tutorials over here:
>> http://ringo.ams.stonybrook.edu/index.php/AMBER_Tutorials
>>
>> On Sat, Jun 20, 2020 at 10:55 AM Rodrigo Galindo-Murillo <
>> rodrigogalindo.gmail.com> wrote:
>>
>>> Hello Sruthi!
>>> Yes, it seems the amber-hub is down, I will see to it.
>>>
>>> Thanks for letting us know.
>>>
>>> Rodrigo.
>>>
>>> On Sat, Jun 20, 2020 at 9:33 AM Sruthi Sudhakar
>>> <sruthisudhakarraji.gmail.com> wrote:
>>>>
>>>> Hello everyone,
>>>>
>>>> Many of the amber tutorials are unavailable. Like the simulation of
>>> nucleic
>>>> acids. Could you please tell how to obtain those tutorials again?
>>>>
>>>> Thank you
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>>
>>
>>
>> *Regards *
>>
>>
>> *PREETI PANDEY (Ph. D.)*
>>
>> -
>>
>>
>> -
>>
>>
>> -
>>
>>
>> -
>>
>> *Postdoctoral Research Associate*
>> *Department of Chemistry & Biochemistry*
>> *University of Oklahoma*
>>
>> *101 Stephenson ParkwayNorman, OK 73019-5251, USA*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 21 Jun 2020 08:58:38 +0200
> From: Ahmed Elrashedy <ahmedelrashedy45.gmail.com>
> Subject: Re: [AMBER] Tutorials unavailable
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAKuX6-da1yZdBOvuMDz6SsLYRB21Gj72XQQgrRWYBKFmc3yXqQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear All
>
> please see the link for Amber-hub
>
> https://amberhub.chpc.utah.edu/
>
>
>
> Thank you and Best regards.
> Ahmed Elrashedy
> Pharmaceutical Chemistry (Ph.D)
> Molecular Modeling and Drug Design Research Group
> Discipline of Pharmaceutical Sciences
> School of Health Science
> University of KwaZulu-Natal
> Westville Campus
> Private Bag X54001
> Durban 4000
> South Africa
> Website: http://soliman.ukzn.ac.za
>
>
>
>
> On Sun, Jun 21, 2020 at 8:09 AM Sruthi Sudhakar <
> sruthisudhakarraji.gmail.com> wrote:
>
>> Thank you all for the response
>>
>> On Sun, Jun 21, 2020 at 12:17 AM Preeti Pandey <preetipandey2806.gmail.com
>>>
>> wrote:
>>
>>> For the time being, you can have a look at the tutorials over here:
>>> http://ringo.ams.stonybrook.edu/index.php/AMBER_Tutorials
>>>
>>> On Sat, Jun 20, 2020 at 10:55 AM Rodrigo Galindo-Murillo <
>>> rodrigogalindo.gmail.com> wrote:
>>>
>>>> Hello Sruthi!
>>>> Yes, it seems the amber-hub is down, I will see to it.
>>>>
>>>> Thanks for letting us know.
>>>>
>>>> Rodrigo.
>>>>
>>>> On Sat, Jun 20, 2020 at 9:33 AM Sruthi Sudhakar
>>>> <sruthisudhakarraji.gmail.com> wrote:
>>>>>
>>>>> Hello everyone,
>>>>>
>>>>> Many of the amber tutorials are unavailable. Like the simulation of
>>>> nucleic
>>>>> acids. Could you please tell how to obtain those tutorials again?
>>>>>
>>>>> Thank you
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> *Regards *
>>>
>>>
>>> *PREETI PANDEY (Ph. D.)*
>>>
>>> -
>>>
>>>
>>> -
>>>
>>>
>>> -
>>>
>>>
>>> -
>>>
>>> *Postdoctoral Research Associate*
>>> *Department of Chemistry & Biochemistry*
>>> *University of Oklahoma*
>>>
>>> *101 Stephenson ParkwayNorman, OK 73019-5251, USA*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 21 Jun 2020 07:53:49 +0000 (UTC)
> From: Ibrahim Mohamed <hollow_ichigo199799.yahoo.com>
> Subject: [AMBER] How to use Ambertools20 parmed.py?
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <1410791556.2459155.1592726029894.mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Greetings sir,I built and installed Ambertools20 but when i tried to run this command:$amberhome/parmed-master/parmed.pyit gave me this error:/parmed-master/parmed.py: No such file or directoryHow can I solve this? And Is this the right command to use parmed.py?Thanks
>
>
> ------------------------------
>
> Message: 7
> Date: Sun, 21 Jun 2020 15:04:04 +0200
> From: Houcemeddine Othman <houcemoo.gmail.com>
> Subject: Re: [AMBER] Incompatibility of coordinate file with topology
> after minimization
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFUV5L9VZN3A4SwVMSm5yA7NuQZhx370nHNH0k7Dqfi8Ns=v-A.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank for the reply,
> I did not know that as I used to work with version 12 of Amber. It is
> indeed a netcdf file.
> The reason why I said they are incompatible, is that I failed to load the
> files in vmd and ambpdb and I though that by specifying the extension will
> be sufficient to write an rst file.
>
> Regards
>
>
> On Sun, Jun 21, 2020 at 3:22 AM David A Case <david.case.rutgers.edu> wrote:
>
>> On Sat, Jun 20, 2020, Houcemeddine Othman wrote:
>>
>>> I am running a restrained minimization step of a
>>> protein+solvent+counterions system using the following input
>>>
>>> minimization parameters
>>> &cntrl
>>> imin = 1, maxcyc = 7000, ncyc = 1000, cut = 12, ntb = 1, ntr = 0, igb = 0,
>>> drms = 0.01
>>> /
>>> sander -O -i energy_min1.in -o energy_min1.out -c sructure_start.rst7 -p
>>> structure.prmtop -r structure_min1.rst7 -ref sructure_start.rst7
>>>
>>> Everything runs successfully. However, the resulting minimized structure
>>> (structure_min1.rst7) contains lesser information (2 Mb) than the starting
>>> structure (sructure_start.rst7, 3Mb). It is also not compatible with the
>>> topology file (structure.prmtop).
>>
>> The default format for restart files is netcdf, which will often by
>> smaller than a formatted form. Use the "file" command to see which
>> files are formatted ("ASCII") and which are not ("data").
>>
>> [The ntxo variable controls the format of restart files; but we
>> recommend sticking with the default unless you know you have a good
>> reason not to.]
>>
>> How did you conclude that the min1 restart file is not compatible with
>> the prmtop file?
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Houcemeddine Othman
> www.bioinfo-on-dunes.net
> Sydney Brenner Institute of molecular bioscience
> University of the Witwatersrand
> The Mount, 9 Jubilee Road,
> Parktown 2193, Johannesburg,
> Gauteng, South Africa.
>
>
> ------------------------------
>
> Message: 8
> Date: Sun, 21 Jun 2020 10:57:26 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] How to use Ambertools20 parmed.py?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200621145726.omk3asxjz7ksczec.rult-wood-l.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Sun, Jun 21, 2020, Ibrahim Mohamed wrote:
>
>> Greetings sir,I built and installed Ambertools20 but when i tried to
>> run this command:$amberhome/parmed-master/parmed.pyit gave me this
>> error:/parmed-master/parmed.py: No such file or directoryHow can I solve
>> this? And Is this the right command to use parmed.py?Thanks
>
> To "run" parmed from the command line, use $AMBERHOME/bin/parmed (no
> ".py" extension).
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Sun, 21 Jun 2020 09:58:34 -0600
> From: Rodrigo Galindo-Murillo <rodrigogalindo.gmail.com>
> Subject: Re: [AMBER] Tutorials unavailable
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEg5OQGTxxrNxgGNfjwi02bAe=B12Ly-oN6FJBEkvB9tE7cb1A.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> The links are available now, the website is restored.
>
> Best,
> Rodrigo.
>
> On Sun, Jun 21, 2020 at 12:09 AM Sruthi Sudhakar
> <sruthisudhakarraji.gmail.com> wrote:
>>
>> Thank you all for the response
>>
>> On Sun, Jun 21, 2020 at 12:17 AM Preeti Pandey <preetipandey2806.gmail.com>
>> wrote:
>>
>>> For the time being, you can have a look at the tutorials over here:
>>> http://ringo.ams.stonybrook.edu/index.php/AMBER_Tutorials
>>>
>>> On Sat, Jun 20, 2020 at 10:55 AM Rodrigo Galindo-Murillo <
>>> rodrigogalindo.gmail.com> wrote:
>>>
>>>> Hello Sruthi!
>>>> Yes, it seems the amber-hub is down, I will see to it.
>>>>
>>>> Thanks for letting us know.
>>>>
>>>> Rodrigo.
>>>>
>>>> On Sat, Jun 20, 2020 at 9:33 AM Sruthi Sudhakar
>>>> <sruthisudhakarraji.gmail.com> wrote:
>>>>>
>>>>> Hello everyone,
>>>>>
>>>>> Many of the amber tutorials are unavailable. Like the simulation of
>>>> nucleic
>>>>> acids. Could you please tell how to obtain those tutorials again?
>>>>>
>>>>> Thank you
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> *Regards *
>>>
>>>
>>> *PREETI PANDEY (Ph. D.)*
>>>
>>> -
>>>
>>>
>>> -
>>>
>>>
>>> -
>>>
>>>
>>> -
>>>
>>> *Postdoctoral Research Associate*
>>> *Department of Chemistry & Biochemistry*
>>> *University of Oklahoma*
>>>
>>> *101 Stephenson ParkwayNorman, OK 73019-5251, USA*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 10
> Date: Sun, 21 Jun 2020 12:35:12 -0400
> From: "Kolattukudy P. Santo" <santotheophys.gmail.com>
> Subject: [AMBER] pH-REMD error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAoy1ooM4rrKF-evJHjdyDhRoFL_L03xQL-4QU4Vz3YB+XgaWA.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello
> I am trying to run pH replica exchange (ph-REMD) simulations with AMBER 18.
> and I am getting an error
> --
> Launching AMBER's PMEMD (Particle Mesh Ewald Molecular Dynamics):
> Checking cpin file and/or cein file.
> We are going to find DELTAGREF for a pH titratable residue using Replica
> Exchange.
> The solvent pH value of replica 1 is 2.000 and was loaded from the
> mdin file (pH2/md1.in).
> The solvent pH value of replica 2 is 2.500 and was loaded from the
> mdin file (pH25/md1.in).
> The solvent pH value of replica 3 is 3.000 and was loaded from the
> mdin file (pH3/md1.in).
> The solvent pH value of replica 4 is 3.500 and was loaded from the
> mdin file (pH35/md1.in).
> The solvent pH value of replica 5 is 4.000 and was loaded from the
> mdin file (pH4/md1.in).
> The target pKa is 3.21000.
> The temperature is 300.00 K and was loaded from the mdin file (pH2/md1.in
> ).
> According to the mdin file (pH2/md1.in), the value of ntcnstph is 5.
> According to the mdin file (pH2/md1.in), the value of nstlim is 100.
> According to the mdin file (pH2/md1.in), the value of numexchg is 5000.
>
> The program will try to find a range of values for DELTAGREF
> automatically, as the argument -dgrefrange was not given
>
> AMBER execution #1: running 5000 MD steps (50 replica exchange attempts)
> for DELTAGREF = 0.000000 kcal/mol
>
> ERROR: The execution of AMBER using the binary
> /projects/community/gcc/5.4/mvapich2/2.2/cuda/9.0/amber/18/kholodvl/bin/pmemd.MPI
> failed. The execution returned the following STDERR:
>
> slurmstepd: error: *** STEP 37153230.0 ON gpu006 CANCELLED AT
> 2020-06-21T12:20:32 ***
>
>
> The command executed was:
>
> srun --kill-on-bad-exit -n 5 --mpi=pmi2
> /projects/community/gcc/5.4/mvapich2/2.2/cuda/9.0/amber/18/kholodvl/bin/pmemd.MPI
> -ng 5 -groupfile groupfile.temporary
>
> Check the mdout file (pH2/md1.out) to see what the error might be.
> Also check if all libraries necessary to run AMBER are properly set.
> The execution of finddgref.py stopped
> NTasks MaxRSS MaxVMSize AveRSS AveVMSize AveCPU Elapsed
> -------- ---------- ---------- ---------- ---------- ---------- ----------
> 00:00:14
> 1 00:00:14
> 5 1664K 352260K 1700659 352260K 00:00:00 00:00:01
> --------------------
>
> No PH2/md1.out was created. What could be the error here ?
>
>
> --
> Best,
> KP Santo
> --------------------------------------------------------------
> Dr. Kolattukudy P. Santo
> Post doctoral Associate
> Department of Chemical and Biochemical Engineering
> Rutgers, The State University of New Jersey
> New Brunswick, New jersey
> USA
> ---------------------------------------------------------
>
>
> ------------------------------
>
> Message: 11
> Date: Sun, 21 Jun 2020 18:17:13 +0000
> From: "Cruzeiro,Vinicius Wilian D" <vwcruzeiro.ufl.edu>
> Subject: Re: [AMBER] pH-REMD error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <DBC54E9D-945A-49EC-A0B2-2BE14CB5BBC7.ufl.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> pH-REMD must be run with an even number of replicas, so you will do either add or remove one pH value. Also, pmemd.MPI needs at least two CPUs per replica, thus the values on the -n flag needs to be at least 2 times the value of your -ng flag.
>
> If you still have problems after fixing that, try to run the pmemd.MPI command directly and see what error you get.
>
> I hope this helps,
> Best,
>
>
> Vin?cius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On Jun 21, 2020, at 9:37 AM, Kolattukudy P. Santo <santotheophys.gmail.com> wrote:
>
> srun --kill-on-bad-exit -n 5 --mpi=pmi2
> /projects/community/gcc/5.4/mvapich2/2.2/cuda/9.0/amber/18/kholodvl/bin/pmemd.MPI
> -ng 5 -groupfile groupfile.temporary
>
> ------------------------------
>
> Message: 12
> Date: Sun, 21 Jun 2020 14:50:54 -0400
> From: "Kolattukudy P. Santo" <santotheophys.gmail.com>
> Subject: Re: [AMBER] pH-REMD error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAoy1oqT=D7oH2NP_4oxiwMHfVVcG88RL5Z__c551P10LkbdZA.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Vinicius, that simply works in this case !
> Santo
>
> On Sun, 21 Jun 2020 at 14:20, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
> wrote:
>
>> Hi,
>>
>> pH-REMD must be run with an even number of replicas, so you will do either
>> add or remove one pH value. Also, pmemd.MPI needs at least two CPUs per
>> replica, thus the values on the -n flag needs to be at least 2 times the
>> value of your -ng flag.
>>
>> If you still have problems after fixing that, try to run the pmemd.MPI
>> command directly and see what error you get.
>>
>> I hope this helps,
>> Best,
>>
>>
>> Vin?cius Wilian D Cruzeiro
>>
>> PhD Candidate
>> Department of Chemistry, Physical Chemistry Division
>> University of Florida, United States
>>
>> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>>
>> On Jun 21, 2020, at 9:37 AM, Kolattukudy P. Santo <santotheophys.gmail.com>
>> wrote:
>>
>> srun --kill-on-bad-exit -n 5 --mpi=pmi2
>>
>> /projects/community/gcc/5.4/mvapich2/2.2/cuda/9.0/amber/18/kholodvl/bin/pmemd.MPI
>> -ng 5 -groupfile groupfile.temporary
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>>
>
>
> --
> Best,
> KP Santo
> --------------------------------------------------------------
> Dr. Kolattukudy P. Santo
> Post doctoral Associate
> Department of Chemical and Biochemical Engineering
> Rutgers, The State University of New Jersey
> New Brunswick, New jersey
> USA
> ---------------------------------------------------------
>
>
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> End of AMBER Digest, Vol 3040, Issue 1
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Received on Sun Jun 21 2020 - 19:30:04 PDT
