[gmx-users] Shake block crossing node boundaries

2009-04-12 Thread Suman Chakrabarty
Hi, I am trying brownian dynamics simulation of a single polymer chain consisting of 100 atoms in vacuum. All bonds are constrained by LINCS. I am trying to use the particle decomposition scheme for parallel run since for a molecule in vacuum domain decomposition seems to be a waste. I am using th

[gmx-users] define atoms

2009-04-12 Thread shahrbanoo karbalaee
Dear justin how do I know,what is the name ofatom 17 in rmsf table of backbone group.? # g_rmsf -f md.xtc -s md.tpr -o traj_rmsfbackbon.xvg -ox traj_avgazrmsfbackbon.pdb # # g_rmsf is part of G R O M A C S: # # God Rules Over Mankind, Animals, Cosmos and Such # @title "RMS fluctuation" @

Re: [gmx-users] Shake block crossing node boundaries

2009-04-12 Thread David van der Spoel
Suman Chakrabarty wrote: Hi, I am trying brownian dynamics simulation of a single polymer chain consisting of 100 atoms in vacuum. All bonds are constrained by LINCS. I am trying to use the particle decomposition scheme for parallel run since for a molecule in vacuum domain decomposition seems t

Re: [gmx-users] define atoms

2009-04-12 Thread Justin A. Lemkul
shahrbanoo karbalaee wrote: Dear justin how do I know,what is the name ofatom 17 in rmsf table of backbone group.? It should be whatever the 17th atom in the analyzed group is. -Justin # g_rmsf -f md.xtc -s md.tpr -o traj_rmsfbackbon.xvg -ox traj_avgazrmsfbackbon.pdb # # g_rmsf is par

[gmx-users] calculating com-com distances.

2009-04-12 Thread Fernando C
Hi list! Is there the possibility of the g_dist program don't provide the correct com-com distances for molecules simulated in triclinic cells under anisotropic pressure? (I've been calculating com-com distances in order to study the clustering of lipids self-assembled. For it, I've written a sim

Re: [gmx-users] Missing VdW Parameters

2009-04-12 Thread darrellk
Hi David, Yes, indeed, the topology file does have the #include statement. Here is an extract from the topology file: *** ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Namenrexcl ICE

Re: [gmx-users] Replica Exchange Error

2009-04-12 Thread Joe Joe
It works just fine without RE. On Sat, Apr 11, 2009 at 8:49 PM, Mark Abraham wrote: > Joe Joe wrote: > >> Hi Justin, >> >> Thanks for helping me with this. >> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Joe Joe wrote: >> >>How do I determine

Re: [gmx-users] Replica Exchange Error

2009-04-12 Thread Mark Abraham
Joe Joe wrote: It works just fine without RE. OK well that sounds like after a replica exchange attempt, some data structure isn't being (re-)constructed correctly. See if you can construct a pair of .tpr files that reproduce the problem with replica exchange after a small number of replica

[gmx-users] Mg ion not recognize.

2009-04-12 Thread akalabya bissoyi
"hello gromacs, i am trying to simulate my protein ligand complex but my protein contains Mg ion and while running Gromacs error is coming in command pdb2gmx.It is not able to recognize Mg ion. I included the coordinates for Mg ion in protein pdb file.And when i included coordinates for Mg ion in l

Re: [gmx-users] Mg ion not recognize.

2009-04-12 Thread Mark Abraham
akalabya bissoyi wrote: "hello gromacs, i am trying to simulate my protein ligand complex but my protein contains Mg ion and while running Gromacs error is coming in command pdb2gmx.It is not able to recognize Mg ion. I included the coordinates for Mg ion in protein pdb file.And when i include

Re: [gmx-users] Replica Exchange Error

2009-04-12 Thread Joe Joe
Will do thanks. Ilya On Sun, Apr 12, 2009 at 7:50 PM, Mark Abraham wrote: > Joe Joe wrote: > >> It works just fine without RE. >> > > OK well that sounds like after a replica exchange attempt, some data > structure isn't being (re-)constructed correctly. See if you can construct a > pair of .tpr