use -cpi state.cpt in the mdrun command
Replace state.cpt file with the actual cpt file written by mdrun.
On Tue, Feb 24, 2015 at 10:39 AM, Abid Channa
wrote:
> Hi gromacs users,
>
> I am working membrane complex simulation of 20
> ns, 100, steps , my simulation is reached 40,0 steps it
Hi gromacs users,
I am working membrane complex simulation of 20
ns, 100, steps , my simulation is reached 40,0 steps it stoped
by mistakenly , How I can extend this 40 lac steps to 1 crore steps
rather than starting , thanks in advance
Abid Ali Channa,
Junior Research Fellow,
Lab No.
Dear all,
I have a Windows 7 OS system which has i7, CPU @ 3.40GHz, 16 GB RAM and newly
installed NVIDIA GeForce GX960 with 1 TB memory.
Since i am familiar with gromacs in Linux system, i am not able to install in
windows environment.
Should i use cygwin or Visual Studio ? Though i tried V
Hi gromacs users,
I am working membrane complex simulation of 20
ns, 100, steps , my simulation is reached 40,0 steps it stoped
by mistakenly , How I can extend this 40 lac steps to 1 crore steps
rather than starting , thanks in advance
Abid Ali Channa,
Junior Research Fellow,
Lab No.
On 2/23/15 6:13 PM, Thomas Lipscomb wrote:
Dear gmx-users,
I have finished the KALP15 in DPPC tutorial up to completing the molecular
dynamics but not any of the
analysis:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/09_analysis.html
I made one chang
Dear gmx-users,
I have finished the KALP15 in DPPC tutorial up to completing the molecular
dynamics but not any of the
analysis:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/09_analysis.html
I made one change to the tutorial: using one maximin 3 molecule
On 2/23/15 9:32 AM, soumadwip ghosh wrote:
Dear all,
I started an MDrun of Barstar protein in TIP3P water and 8M
urea, neutralized by the required number of counterions. Until the mdrun,
there was no issue with either energy minimization and equilibration steps.
But whenever I wan
Hi Soumadwip,
I my understanding this error occurs when GROMACS can't distribute your job
on the number of cores you are asking. Try to change the number of cores
from 80 to something else, probably a fewer number of cores.
I had this error once and I figured out that was the reason, but I am not
Dear all,
I started an MDrun of Barstar protein in TIP3P water and 8M
urea, neutralized by the required number of counterions. Until the mdrun,
there was no issue with either energy minimization and equilibration steps.
But whenever I want to start MD run, a fatal error shows up saying
On 2/23/15 3:47 AM, Peter Kroon wrote:
On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote:
Thanks for your reply Dr. Lemkul
I changed the bond length to zero in my topology file, forcefield file and
in the n2t file. I also added the [ exclusion] section-
If memory serves, you don't need a bo
On 2/23/15 6:50 AM, leila salimi wrote:
Dear all,
I have a question regarding radial distribution function. Does g_rdf
program work for non-cubic cell eg. triclinic?
Yes.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdo
On 2/23/15 1:04 AM, marzieh dehghan wrote:
Hi every body
1- In the phosphate group, we have 4 oxygen atoms that bond to the
phosphate. Two of them are as follow: CH2-O-P-OH and the others include:
- A double bond is on the top of phosphor atom
- A OH group is at the b
On 2/23/15 12:12 AM, rahul dhakne wrote:
Dear Gromacs user,
I am running mdrun to minimize (energy minimization) my structure
co-ordinate, but every time it stuck by displaying following error
Back Off! I just backed up em.log to ./#em.log.8#
Reading file em.tpr, VERSION 5.0.4 (single pre
Dear all,
I have a question regarding radial distribution function. Does g_rdf
program work for non-cubic cell eg. triclinic?
Regards,
Leila
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On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote:
> Thanks for your reply Dr. Lemkul
>
> I changed the bond length to zero in my topology file, forcefield file and
> in the n2t file. I also added the [ exclusion] section-
If memory serves, you don't need a bond between a shell particle and
it's "
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