Hi there.
Lately I've been running simulations using GPUs on a computer node.
I noticed that though the GPUs are always in use sometimes I don't get
this message in the output:
Using 4 MPI threads
Using 2 OpenMP threads per tMPI thread
4 GPUs detected:
#0: NVIDIA Tesla C2070, compute cap.: 2.0
Yes. It may be more efficient to group them into a trajectory before
calling mdrun.
Mark
On Aug 2, 2013 7:29 AM, "tarak karmakar" wrote:
> Thank you Mark.
>
> So, if I got it properly, for my system (dihedral scanning), I need to
> generate configurations, manually, and then perform this 'single
What does gmxcheck say about them?
On Aug 2, 2013 8:08 AM, "Shine A" wrote:
> Sir,
>
> I did an 80 ns Remd simulation, after completion of the simulation
> extended it up to 480 ns using tpbconv. Now the extended trajectories also
> write on old trajectory files(traj.trr)?
> --
> gmx-users m
On Fri, Aug 2, 2013 at 4:48 AM, Trayder wrote:
> Hi all,
> I've been running an analysis of the same system (protein/ligand/water/ions)
> using multiple timesteps (1-5fs) to identify differences in behaviour
> between the settings. To do this I've compared the energy outputs of the 5
> simulations
oh, sorry.
So the error is:
Fatal error:
Topology include file "posre.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
My topo
On 8/2/13 5:57 AM, chinnu657 wrote:
oh, sorry.
So the error is:
Fatal error:
Topology include file "posre.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
There are probably #include statements
On 8/2/13 2:04 AM, Venkat Reddy wrote:
Thanks Justin for the quick reply. I am simulating a protein with bound
lipids. I am in a dilemma to choose the direction of the normal to
calculate order parameter. In your *Membrane-protein *simulation tutorial,
you have chosen normal to the bilayer alon
Hi Justin,
Yes that was a problem. So after modifying my #include statement in the itp
file (initially top. file), it became:
; Include Position restraint file
#ifdef POSRES
#include "posre_2CDS.itp"
#endif
thank you
Chinnu
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If i understand the problem correctly, you can plot the com of any group of
atoms as a function of time with g_traj. Create an index file of whatever
atoms you want using make_ndx then use g_traj with -com flag to plot com of
the group.
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On Thu, Aug 1, 2013 at 10:10 PM, akk5r wrote:
> Hi All,
>
> I am trying to run a membrane protein simulation on Gromacs 4.6 using the
> Charmm 36 force field parameters.
>
> I found the following parameters on the gromacs mailing list for Charmm 36:
> *; nblist cut-off
> rlist=
Hello
thanks for the answer
I've tried this option, but the obtained result is the g_potential with the
popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5,
region corresponding to "water" phase at z=3.5 and the other one monolayer
from 3.5 to 7. In fact lipid bilayer core is at z
On 8/2/13 10:33 AM, wood irene wrote:
Hello
thanks for the answer
I've tried this option, but the obtained result is the g_potential with the
popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5,
region corresponding to "water" phase at z=3.5 and the other one monolayer
from 3.
Sir,
But if something went wrong, then "over" is rather irrelevant, isn't it?
Yes. I am planning to rerun ifI dont get any solution.
> So your simulation started from some previous point and re-ran? I don't
> see how this would be possible given what you have been posting.
The overlap was
Hi,
I performed 2 simulations of a lysozyme in water: one with the version 4.5
of Gromacs and another with the version 4.6.1 (I used the exact same
inputs).
Then I calculated the MSD and I obtained a complete different behavior with
the version 4.6.1 of Gromacs and this MSD is obviously wrong.
<
1ns is rather an eyeblink, and MD is chaotic... what is your evidence
that the trend of RMSD either run is representative?
Mark
On Fri, Aug 2, 2013 at 5:50 PM, Guillaume Chevrot
wrote:
> Hi,
>
> I performed 2 simulations of a lysozyme in water: one with the version 4.5
> of Gromacs and another w
Thanks for your notes.
I did a diagnosis test which could be of relevance here.
I set up the following system:
[ gas | liquid water (solid water) liquid water | gas ]
gas is united atom methane.
liquid water is tip4p-ice model and solid water is a cage-like crystalline
structure of water and me
Hi, are you referring to the MSD of the protein?
I am not sure which of the MSDs are right, or why there is a difference
between the two versions. But, both of the MSDs are plausible. There is no
obvious wrong answer. Complex molecules have a long time relaxation and may
exhibit glassy behavior and
On 8/2/13 3:19 PM, S. Alireza Bagherzadeh wrote:
Thanks for your notes.
I did a diagnosis test which could be of relevance here.
I set up the following system:
[ gas | liquid water (solid water) liquid water | gas ]
gas is united atom methane.
liquid water is tip4p-ice model and solid water
Hi all,
I went through the manual and couldn't find any definite answers to the
following questions.
First, I wonder if the reference positions of position restraints, not just
the force constants, of different replicas are exchanged in hamiltonian
exchange based on restraint-lambdas? For example
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