Re: [gmx-users] shell MD

2013-07-05 Thread Dr. Vitaly Chaban
Vitaly saw this problem while running gromacs/mopac interface about 4 years ago... The impression was that the problem is related to incorrectly computed forces. I would file a bug report. Dr. Vitaly V. Chaban On Fri, Jul 5, 2013 at 2:43 PM, Sergey wrote: > Possibly, can :) > I will have t

Re: [gmx-users] shell MD

2013-07-05 Thread Sergey
Possibly, can :) I will have to run shell MD in NAMD, though it will be slower a bit. Seemingly, only Vitaly see my problem :). 05.07.2013, 16:31, "Dr. Vitaly Chaban" : > The was a bug report on this error a few years ago, > http://redmine.gromacs.org/issues/332 > > Can your problem correlate wit

Re: [gmx-users] shell MD

2013-07-05 Thread Dr. Vitaly Chaban
The was a bug report on this error a few years ago, http://redmine.gromacs.org/issues/332 Can your problem correlate with that discussion, perhaps? Dr. Vitaly V. Chaban On Fri, Jul 5, 2013 at 1:58 PM, Sergey wrote: > In case of MD run. Minimization procedure was successful. > > 05.07.2013,

Re: [gmx-users] shell MD

2013-07-05 Thread Sergey
In case of MD run. Minimization procedure was successful. 05.07.2013, 14:48, "Dr. Vitaly Chaban" : > In which case can the determinant not be computed? > > Dr. Vitaly V. Chaban > > On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote: > >>  Dear users, >> >>  I'm trying to run MD with SWM4-DP model (dat

Re: [gmx-users] shell MD

2013-07-05 Thread Dr. Vitaly Chaban
In which case can the determinant not be computed? Dr. Vitaly V. Chaban On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote: > Dear users, > > I'm trying to run MD with SWM4-DP model (data from > http://virtualchemistry.org), but I always have error: > "Can not invert matrix, determinant =". > > I

Re: [gmx-users] shell MD

2013-07-04 Thread Sergey
My .mdp file is following: title= spce cpp = /lib/cpp integrator = md cutoff-scheme= verlet nsteps = 5 nstlist = 10 dt = 0.001 pbc = xyz coulombtype

[gmx-users] shell MD

2013-07-04 Thread Sergey
Dear users, I'm trying to run MD with SWM4-DP model (data from http://virtualchemistry.org), but I always have error: "Can not invert matrix, determinant =". I did energy minimization etc. but it don't help... May be someone have complete stuff of files for shell MD, including .mdp file ? Serge

Re: [gmx-users] Shell MD

2011-11-06 Thread David van der Spoel
On 2011-11-06 12:23, yiran870804 wrote: *Dear sir： * ** *Thank you for reading my letter. * *I have a few problems in Shell MD . I have set the parameter of Shell MD as the Gromacs manualin my *.mdp file. * _/emtol:10.0 use 0.001 instead. one processor only for the time being. niter:

[gmx-users] Shell MD

2011-11-06 Thread yiran870804
Dear sir： Thank you for reading my letter. I have a few problems in Shell MD . I have set the parameter of Shell MD as the Gromacs manual in my *.mdp file. emtol:10.0 niter:20 fcstep:0 But the result is the same with the traditilnal MD. Whether the Gromacs can not finish

[gmx-users] Shell MD

2011-11-04 Thread yiran870804
Dear sir： Thank you for reading my letter. I have a few problems in Shell MD . I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help. And this is my own *.mdp file below emtol= 10 emstep = 0.01 n

[gmx-users] Shell MD

2011-11-04 Thread yiran870804
Dear sir： Thank you for reading my letter. I have a few problems in Shell MD . I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help. And this is my own *.mdp file below include = define = integrat