Dear All
I am trying to perform the azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp level which was
327 non-matching atom names
atom names from azide.top will be used
atom names
On 8/21/12 6:00 AM, Deepak Ojha wrote:
Dear All
I am trying to perform the azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp level which was
327 non-matching atom names
atom
Dear gmx-users:
Thanks Justin for your help. But now I am experiencing a Segmentation fault
error when executing mdrun. I've perused the archives but found none of the
threads on segmentation faults similar to my case here. I believe the
segmentation fault is caused by the awkward
rainy908 wrote:
Dear gmx-users:
Thanks Justin for your help. But now I am experiencing a Segmentation fault
error when executing mdrun. I've perused the archives but found none of the
threads on segmentation faults similar to my case here. I believe the
segmentation fault is caused by
Hi Justin,
THanks for the input. So I traced back to my energy minimization steps, and am
getting the error message after I execute the following line:
$mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr
output:
Back Off! I just backed up md.log to ./#md.log.2#
Reading file
On 18/08/2011 2:41 PM, rainy908 wrote:
Hi Justin,
THanks for the input. So I traced back to my energy minimization steps, and am
getting the error message after I execute the following line:
$mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr
output:
Back Off! I just backed up
On Feb 23, 2009, at 9:22 AM, Nikit sharan wrote:
Dear justin,
As you suggested i have changed the coloumb type to PME and set
pme_order to 5 as said in the mailing list as it will increase the
Hi Nikit,
I think pme_order should be an even number in gromacs. You might
want to try with order
Nikit sharan wrote:
Dear justin,
As you suggested i have changed the coloumb type to PME and set
pme_order to 5 as said in the mailing list as it will increase the
Try an even number.
accuracy.But then the simulation is not getting completed.Its taking
hours together.Normally what's the
Hello sir,
Thanks for your suggestion.Then as u suggested i start the work from
scratch and did the equilibriation again, there is nothing wrong with
the topology also because it was taken from tiemann's website.The only
message that it gives after equlibriation run is
Steepest Descents
Nikit sharan wrote:
Hello sir,
Thanks for your suggestion.Then as u suggested i start the work from
scratch and did the equilibriation again, there is nothing wrong with
the topology also because it was taken from tiemann's website.The only
message that it gives after equlibriation run is
Mark Abraham wrote:
coulombtype = Cut-off
In addition to everything Mark said, you should also *never* run a bilayer
simulation with a simply cutoff scheme. You will get terrible artefacts. That
goes for most other simulations too, but it has been demonstrated very recently
Arneh Babakhani
Date: mar. 2006-05-02 23:21
À: Discussion list for GROMACS users
Objet : Re: RE : [gmx-users] segmentation fault in mdrun when using PME
Hello, I'm experiencing the exact same problem, when trying to do some
restrained molecular dynamics of a small peptide in a water box. Have you
-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Sat 4/29/2006 2:25 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] segmentation fault in mdrun when using PME
Diane Fournier wrote:
Hi, I'm new to Gromacs and I'm trying to run
Diane Fournier wrote:
-Original Message-
From: [EMAIL PROTECTED] on behalf of David van der Spoel
Sent: Sat 4/29/2006 2:25 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] segmentation fault in mdrun when using PME
Diane Fournier wrote:
Hi, I'm new to Gromacs
Diane Fournier wrote:
Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex
molecular dynamics simulation. I have tried doing John
Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation
fault and core dump at the steepest descents minimization step. However,
mdrun
Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand
complex molecular dynamics simulation. I have tried doing John
Kerrigan'sDrug-Enzyme tutorial and mdrun crashes withsegmentation
fault and core dump at the steepest descents minimization step. However, mdrun
works fine when using
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