From: nader zabarjad (zabarjad_sh_at_yahoo.com)
Date: Sun Aug 02 2015 - 10:41:55 CDT
Dear NAMD usersI try to run minimization and MD for a polymer in water box at NVT. The final pressure I got was 3760. I am not sure if this is an acceptable or it is huge.I really appreciate any comment
Regards
Nader
On Sunday, August 2, 2015 2:56 AM, namd-l digest <owner-namd-l-digest_at_ks.uiuc.edu> wrote:
namd-l digest Saturday, August 1 2015 Volume 01 : Number 1726
In this issue:
namd-l: sausage plot for a namd trajectory in vmd
Re: namd-l: sausage plot for a namd trajectory in vmd
namd-l: Re: how to create two namd jobs in a single script with 2 x dual cuda gpus?
----------------------------------------------------------------------
Date: Fri, 31 Jul 2015 12:01:02 +0200
From: luca belmonte <lucabelmonte_at_gmail.com>
Subject: namd-l: sausage plot for a namd trajectory in vmd
Dear all,
I have to represent fluctuations of small molecules around prostetic group.
I began with the time step, as showed in many namd tutorials, but this is
unsatisfactory for this specific case.
So, I was wondering if there is a way to represent the whole trajectory as
a sausage plot, like the ones usually used for NMR.
Could you share your experience regarding this issue with me?
Thank you for all your comments,
Best regards,
Luca
- --
Luca Belmonte, PhD
CIBIO - Center for Integrative Biology
University of Trento
Phone: +39 0461 28 53 41
Mobile: +39 328 45 81 762
------------------------------
Date: Fri, 31 Jul 2015 06:44:17 -0400
From: Aaron Larsen <alarsen_at_molbio.mgh.harvard.edu>
Subject: Re: namd-l: sausage plot for a namd trajectory in vmd
Hi Luca,
"So, I was wondering if there is a way to represent the whole trajectory as
a sausage plot, like the ones usually used for NMR."
Yes, there is! This is done through vmd. You need to load a trajectory file
(dcd), add labels to the bonds, angles, torsions etc. that you want to
monitor and then have them exported to a graph as as function of the time
stamp, The best way to do this is with a tcl script. I will email you an
example script once I am at my work pc.
Best,
Aaron
On Fri, Jul 31, 2015 at 6:01 AM, luca belmonte <lucabelmonte_at_gmail.com>
wrote:
> Dear all,
>
> I have to represent fluctuations of small molecules around prostetic group.
> I began with the time step, as showed in many namd tutorials, but this is
> unsatisfactory for this specific case.
>
> So, I was wondering if there is a way to represent the whole trajectory as
> a sausage plot, like the ones usually used for NMR.
>
> Could you share your experience regarding this issue with me?
>
> Thank you for all your comments,
> Best regards,
> Luca
>
>
> --
> Luca Belmonte, PhD
>
> CIBIO - Center for Integrative Biology
> University of Trento
>
> Phone: +39 0461 28 53 41
> Mobile: +39 328 45 81 762
>
- --
Aaron Larsen, Ph.D.
Harvard University Department of Chemistry and Chemical Biology
Harvard Medical School Department of Genetics
E-mail: alarsen_at_molbio.mgh.harvard.edu
Mobile: 617-319-3782
FAX: 617-643-3328
------------------------------
Date: Sat, 1 Aug 2015 14:33:04 -0700
From: nam kim <namkkim_at_gmail.com>
Subject: namd-l: Re: how to create two namd jobs in a single script with 2 x dual cuda gpus?
On Sat, Aug 1, 2015 at 1:51 PM, nam kim <namkkim_at_gmail.com> wrote:
> computing node has 32 cores with 4 GTX 980 gpus.
> with CUDA_VISIBLE_DEVICES, I'd like to run two namd jobs with a pair of
> gpus. script below I wrote failed. Could you help me to find errors?
> --------------------------------------------------
>
> #!/bin/bash
> #SBATCH -D /home/rhye
> #SBATCH -J grk4-R65L
> #SBATCH --partition=gpus
> #SBATCH --get-user-env
> #SBATCH --nodes=1
> #SBATCH --ntasks-per-node=2
> #SBATCH --gres=gpu:2
> #SBATCH --time=00:30:00
>
> source /etc/profile.d/modules.sh
> srun hostname -s | sort -u >slurm.hosts
>
> CUDA_HOME=/cm/shared/apps/cuda70/toolkit/current
> export NAMD_HOME=/home/namkim/NAMD-GPU/bin
> export PATH=$CUDA_HOME/bin:$NAMD_HOME:$PATH
> export LD_LIBRARY_PATH=$CUDA_HOME/lib64:$NAMD_HOME:$LD_LIBRARY_PATH
> export CUDA_VISIBLE_DEVICES=0,1
>
> cd /home/rhye/R65L-SIMULATION
> export NAMD_JOBNAME=/home/rhye/R65L-SIMULATION
>
> srun $NAMD_HOME/charmrun ++local +p16 $NAMD_HOME/namd2 +idlepoll +devices
> $CUDA_VISIBLE_DEVICES newer-sample5.conf >& speed-testx1.log &
>
>
>
> export CUDA_VISIBLE_DEVICES=2,3
>
> srun $NAMD_HOME/charmrun ++local +p16 $NAMD_HOME/namd2 +idlepoll +devices
> $CUDA_VISIBLE_DEVICES newer-sample5.conf >& speed-testx2.log &
>
> wait
>
>
> rm -f slurm.hosts
>
>
------------------------------
End of namd-l digest V1 #1726
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