Re: [gmx-users] Onw question about rlist rvdw rcoulomb and nstlist

xuji wrote: > Dear all gromacs users: > > Usually when we do neighbour searching we should give three parameters: > cut-off distance, buffer length and > the frequency of the neighbour list updating. But in Gromacs *.mdp file it's > just required to give rlist,nstlist, > rvdw and rcoumlomb. Wh

[gmx-users] Onw question about rlist rvdw rcoulomb and nstlist

Dear all gromacs users: Usually when we do neighbour searching we should give three parameters: cut-off distance, buffer length and the frequency of the neighbour list updating. But in Gromacs *.mdp file it's just required to give rlist,nstlist, rvdw and rcoumlomb. Where is the buffer length o

Re: [gmx-users] unit of the opls-aa force field in Gromacs package

sunny...@gmail.com wrote: Hello Could someone tell me what are the exact units of the force constants of bond and angle term of the OPLS-aa force field implemented in the Gromacs package? Table 5.4 in the manual. -Justin Thank you in advance Sunjoo --

[gmx-users] unit of the opls-aa force field in Gromacs package

Hello Could someone tell me what are the exact units of the force constants of bond and angle term of the OPLS-aa force field implemented in the Gromacs package? Thank you in advance Sunjoo ___ gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] problem with running mdrun in parallel

Hi there, I am trying to run an MD simulation on a 13 residue peptide with distance restraints. Before, I ran into a problem with this system when an error message occurred during mdrun concerning distance restraints and domain decomposition. There was apparently a bug in mshift.c and the bug was

Re: [gmx-users] minimization problem

Hongyan Xiao wrote: Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! You

Re: [gmx-users] minimization problem

Hongyan Xiao wrote: Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks!

[gmx-users] minimization problem

Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! H. Y. Xiao _

Re: [gmx-users] Forces are large - How to track down the culprit

Hi Shay, sorry for the late comment - let me guess, you compiled Gromacs in double precision? :) Greetings Steffen > < Is this reproducible? > Yes. I've taken the same simulation and had it re-run and got the same error > at the exact same frame (frame 693, which is timeframe 6930). > > I did so

Re: [gmx-users] minimization problem

Hongyan Xiao wrote: Hi, David van der Spoel I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is the em.mdp file. Then the minimization works correctly. See chapter 3 in the manual. ; ; User xiao ; 2008.9.2

[gmx-users] minimization problem

Hi, David van der Spoel I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is the em.mdp file. ; ; User xiao ; 2008.9.28 10:23 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXI

Re: [gmx-users] eigenvalues

On Thu, 8 Jan 2009 16:31:01 +0530 (IST) sanja...@iitb.ac.in wrote: dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the

[gmx-users] eigenvalues

dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenv

Re: [gmx-users] minimization problems

Hongyan Xiao wrote: Hi, gmx-users, I built a system,decane(42molecule)/water(903)/decane(42), including the two decane/water interfaces. However, when I minimized this system, I found the system turn into water/decane(84)/water. That is to say in the initial system two parts of decane turn

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

Hi Berk, I tried this fix, but mdrun_mpi is still hanging. I'll try to use the debugger by the end of the week and let you know. Cheers, Patrick Berk Hess a écrit : Hi, My guess is that this is not the problem. But it is very easy to try, so please do. The diff for src/gmxlib/pbc.c is: 392c3

[gmx-users] minimization problems

Hi, gmx-users, I built a system,decane(42molecule)/water(903)/decane(42), including the two decane/water interfaces. However, when I minimized this system, I found the system turn into water/decane(84)/water. That is to say in the initial system two parts of decane turn into a part, while wate