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-- Necmettin Pirinccioglu (BSc, PhD) Department of Chemistry University of Dicle 21280 Diyarbakir TURKEY ------------------------------ Message: 9 Date: Thu, 25 Feb 2016 01:00:15 -0800 From: Ross Walker <ross.rosswalker.co.uk> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion To: AMBER Mailing List <amber.ambermd.org> Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk> Content-Type: text/plain; charset=us-ascii Hi Necmettin, A few notes here. Firstly it is best to run a small number of steps say nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is going wrong and visualize the trajectory. Also, tempi=600 is hot - that may causes issues - especially if your system is not well equilibrated first. Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable potential function. I would not recommend going above ntf=2,ntc=2 for anything other than debugging. If changing to ntc=2,ntf=2 does not fix things then look carefully at your structure - it may not be well enough minimized, it may have structural deficiencies etc. Visualizing for and ntwx=1 run will help here. The parameters may also be suspect since this is not a regular amino / nucleic acid - where did you get the parameters from? All the best Ross Dear Ross, thanks for your kind reply. well firstly i did try with ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have employed a shorter period. the trajectories indicate that the structure collapses and the mds are ended with the error after a while. please find the md trajectories as attached. I have done these calculations even at 700 K but it worked fine with other small molecules. but i have just got this with phosphoric acid. GAFF parameters were applied for the calculations... best wishes, necmettin -- Necmettin Pirinccioglu (BSc, PhD) Department of Chemistry University of Dicle 21280 Diyarbakir TURKEY -------------- next part -------------- A non-text attachment was scrubbed... Name: mdcrd.tar.gz Type: application/x-gzip Size: 344707 bytes Desc: not available Url : http://lists.ambermd.org/mailman/private/amber/attachments/20160303/ae36aeec/attachment-0001.gz ------------------------------ Message: 5 Date: Thu, 3 Mar 2016 01:22:43 -0800 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion To: AMBER Mailing List <amber.ambermd.org> Message-ID: <56D80263.7070907.cgl.ucsf.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Do you have a successful run previously where you warmed up your system to 600K? I would try setting ntpr and ntwx to 1 and look at the result. Apparently the bond between atoms 1 and 2 is being stressed too much. You may need a shorter time step for such a high temperature. Bill On 3/3/16 12:49 AM, necmettin pirinccioglu wrote: > ---------- Forwarded message ---------- > From: necmettin pirinccioglu <pirincn.gmail.com> > Date: Mon, Feb 29, 2016 at 9:56 AM > Subject: Re: problem running MD for diphosphoric acid anion > To: AMBER Mailing List <AMBER.ambermd.org> > > > > To: AMBER Mailing List <amber.ambermd.org> > > > Dear All, > I have been running MD for diphosphoric acid anion with the following input > but I get the error message below. Helps will be welcomed! > > INPUT > &cntrl > imin=0, irest=1, ntx=5, > nstlim=250000, dt=0.002, > ntc=4, ntf=4, > ntt=1, tautp=0.5, > tempi=600.0, temp0=600.0, > ntpr=500, ntwx=500, > ntb=0, igb=0, > cut=999 > / > > ERROR MESSAGE!!! > --------------------------------------------------- > | Local SIZE OF NONBOND LIST = 1 > | TOTAL SIZE OF NONBOND LIST = 1 > vlimit exceeded for step 369; vmax = 22.0998 > vlimit exceeded for step 373; vmax = 54.3352 > > Coordinate resetting (SHAKE) cannot be accomplished, > deviation is too large > NITER, NIT, LL, I and J are : 0 0 1 1 2 > > -- > Necmettin Pirinccioglu (BSc, PhD) > Department of Chemistry > University of Dicle > 21280 Diyarbakir > TURKEY > > > ------------------------------ > > Message: 9 > Date: Thu, 25 Feb 2016 01:00:15 -0800 > From: Ross Walker <ross.rosswalker.co.uk> > Subject: Re: [AMBER] problem running MD for diphosphoric acid anion > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk> > Content-Type: text/plain; charset=us-ascii > > Hi Necmettin, > > A few notes here. Firstly it is best to run a small number of steps say > nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is > going wrong and visualize the trajectory. > > Also, tempi=600 is hot - that may causes issues - especially if your system > is not well equilibrated first. > > Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable > potential function. I would not recommend going above ntf=2,ntc=2 for > anything other than debugging. > > If changing to ntc=2,ntf=2 does not fix things then look carefully at your > structure - it may not be well enough minimized, it may have structural > deficiencies etc. Visualizing for and ntwx=1 run will help here. > > The parameters may also be suspect since this is not a regular amino / > nucleic acid - where did you get the parameters from? > > All the best > Ross > > Dear Ross, thanks for your kind reply. well firstly i did try with > ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have employed > a shorter period. the trajectories indicate that the structure collapses > and the mds are ended with the error after a while. please find the md > trajectories as attached. I have done these calculations even at 700 K but > it worked fine with other small molecules. but i have just got this with > phosphoric acid. GAFF parameters were applied for the calculations... best > wishes, necmettin > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 6 Date: Thu, 3 Mar 2016 16:37:13 +0530 From: chandan patel <chandanz.gmail.com> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAOiU=0pM6NmzUL9kcb5Buwvmog_gnrZAT87S4CMwts_iivo1og.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hey, Smaller time step may help. On Mar 3, 2016 2:52 PM, "Bill Ross" <ross.cgl.ucsf.edu> wrote: > Do you have a successful run previously where you warmed up your system > to 600K? I would try setting ntpr and ntwx to 1 and look at the result. > Apparently the bond between atoms 1 and 2 is being stressed too much. > You may need a shorter time step for such a high temperature. > > Bill > > On 3/3/16 12:49 AM, necmettin pirinccioglu wrote: > > ---------- Forwarded message ---------- > > From: necmettin pirinccioglu <pirincn.gmail.com> > > Date: Mon, Feb 29, 2016 at 9:56 AM > > Subject: Re: problem running MD for diphosphoric acid anion > > To: AMBER Mailing List <AMBER.ambermd.org> > > > > > > > > To: AMBER Mailing List <amber.ambermd.org> > > > > > > Dear All, > > I have been running MD for diphosphoric acid anion with the following > input > > but I get the error message below. Helps will be welcomed! > > > > INPUT > > &cntrl > > imin=0, irest=1, ntx=5, > > nstlim=250000, dt=0.002, > > ntc=4, ntf=4, > > ntt=1, tautp=0.5, > > tempi=600.0, temp0=600.0, > > ntpr=500, ntwx=500, > > ntb=0, igb=0, > > cut=999 > > / > > > > ERROR MESSAGE!!! > > --------------------------------------------------- > > | Local SIZE OF NONBOND LIST = 1 > > | TOTAL SIZE OF NONBOND LIST = 1 > > vlimit exceeded for step 369; vmax = 22.0998 > > vlimit exceeded for step 373; vmax = 54.3352 > > > > Coordinate resetting (SHAKE) cannot be accomplished, > > deviation is too large > > NITER, NIT, LL, I and J are : 0 0 1 1 2 > > > > -- > > Necmettin Pirinccioglu (BSc, PhD) > > Department of Chemistry > > University of Dicle > > 21280 Diyarbakir > > TURKEY > > > > > > ------------------------------ > > > > Message: 9 > > Date: Thu, 25 Feb 2016 01:00:15 -0800 > > From: Ross Walker <ross.rosswalker.co.uk> > > Subject: Re: [AMBER] problem running MD for diphosphoric acid anion > > To: AMBER Mailing List <amber.ambermd.org> > > Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk> > > Content-Type: text/plain; charset=us-ascii > > > > Hi Necmettin, > > > > A few notes here. Firstly it is best to run a small number of steps say > > nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is > > going wrong and visualize the trajectory. > > > > Also, tempi=600 is hot - that may causes issues - especially if your > system > > is not well equilibrated first. > > > > Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable > > potential function. I would not recommend going above ntf=2,ntc=2 for > > anything other than debugging. > > > > If changing to ntc=2,ntf=2 does not fix things then look carefully at > your > > structure - it may not be well enough minimized, it may have structural > > deficiencies etc. Visualizing for and ntwx=1 run will help here. > > > > The parameters may also be suspect since this is not a regular amino / > > nucleic acid - where did you get the parameters from? > > > > All the best > > Ross > > > > Dear Ross, thanks for your kind reply. well firstly i did try with > > ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have > employed > > a shorter period. the trajectories indicate that the structure collapses > > and the mds are ended with the error after a while. please find the md > > trajectories as attached. I have done these calculations even at 700 K > but > > it worked fine with other small molecules. but i have just got this with > > phosphoric acid. GAFF parameters were applied for the calculations... > best > > wishes, necmettin > > Dear Bill, thank you for your advise... well I did it for shorter steps as also suggested by Ross... the structure eventually collapses. I did many calculations for small and medium size molecules at high temperatures using gaff but i did not get this error with these calculations. I think there is something wrong with phosphoric acid parameters...best wishes, necmettin PS. Dear Professor Case, thanks for your comment. yes indeed the previous message was seen as spam...np -- Necmettin Pirinccioglu (BSc, PhD) Department of Chemistry University of Dicle 21280 Diyarbakir TURKEY _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Mar 16 2016 - 01:00:03 PDT