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
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"
@
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
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
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
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
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
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
"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
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
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
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