Hi,
I have some doubt regarding REMD simulation.
1. In the .mdp file of each replica is it necessary to keep the
gen-temp constant?
as example: 300 k is the lowest temp of REMD simulation. Is it necessary to
keep the gen-temp=300 in each replica.
2. Is it necessary to provide -replex
Thanks Sir,
I did like that only, Now how can I make the distribution plot for these
vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But
results is not proper. Can you suggest me regarding this?
Thank you
On Tue, Jul 30, 2019, 17:27 David van der Spoel
wrote:
> Den
On Tue, Jul 30, 2019 at 3:29 PM Carlos Navarro
wrote:
>
> Hi all,
> First of all, thanks for all your valuable inputs!!.
> I tried Szilárd suggestion (multi simulations) with the following commands
> (using a single node):
>
> EXE="mpirun -np 4 gmx_mpi mdrun "
>
> cd $WORKDIR0
> #$DO_PARALLEL
>
Hi all
I have been having trouble setting up a peptide+water simulation system due
to the appearance of clashes in an energy minimization.
Trying to pin down the origin of the problem I have found that a minimum
system that reproduces my problem is a box with multiple copies of an
unblocked
Hi all,
First of all, thanks for all your valuable inputs!!.
I tried Szilárd suggestion (multi simulations) with the following commands
(using a single node):
EXE="mpirun -np 4 gmx_mpi mdrun "
cd $WORKDIR0
#$DO_PARALLEL
$EXE -s 4q.tpr -deffnm 4q -dlb yes -resethway -multidir 1 2 3 4
And I
Den 2019-07-30 kl. 07:55, skrev Omkar Singh:
Hi,
I did by "gmx gangle ..." command. But I am not getting good result,
because I have a doubt in ndx file. Can you help me for making ndx file.
How should I select the atom for vectors.
For OH it should be
1 2
1 3
4 5
4 6
7 8
7 9
etc., assuming
Kevin, Mark,
thanks for sharing advices and experience.
I am facing some strange behaviour trying to run with the two gpus: there
are some combinations that "simply" make the system crash (the workstation
turns off after few seconds of running); in particular the following runs:
gmx mdrun -deffnm
