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
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, 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
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
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
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.
<
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
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.
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 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=
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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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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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
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
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 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
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
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
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
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