On 8/8/14, 9:18 PM, Abu Naser wrote:
Thanks Justin for your response.
I just manually inserted the input values only to that part of the script. The
atom types I am interested in, they are not available in the charmm36. Since I
have only few unusual atom types, I wish to do them
On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote:
Dear gmx users,
I am new user of gromacs. Our calculations are running, but we have a problem
that has not enough disk space. Therefore I need to delete some file that are
unimportant for analysis. Is there any analysis use trr file? Can I
Hi,
You mean no matter we use GPU acceleration or not, -npme is just a
reference?
Why we can't set that to a exact value?
On 8/9/2014 5:14 AM, Mark Abraham wrote:
You can set the number of PME-only ranks with -npme. Whether it's useful is
another matter :-) The CPU-based PME offload and the
Thank you Justin.
On Saturday, August 9, 2014 5:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote:
Dear gmx users,
I am new user of gromacs. Our calculations are running, but we have a problem
that has not enough disk space. Therefore I need to
Thank you Justin. This is very useful for me. I have a question regarding
(and by -1 since CHARMM specifies these values as negative, but Gromacs uses a
different convention)
I have been wondering what is the Gromacs' convention. Is it just the +ve
value after conversion?
Date:
On 8/9/14, 4:35 AM, Abu Naser wrote:
Thank you Justin. This is very useful for me. I have a question regarding
(and by -1 since CHARMM specifies these values as negative, but Gromacs uses a
different convention)
I have been wondering what is the Gromacs' convention. Is it just the
Thanks a lot Justin, you have been very helpful.
Date: Sat, 9 Aug 2014 05:02:20 -0600
From: jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Charmm to gromacs
On 8/9/14, 4:35 AM, Abu Naser wrote:
Thank you Justin. This is very useful for me. I have a
yes you can delete .trr files since they will not be of any use. they are
not useful during analysis also...
On Sat, Aug 9, 2014 at 3:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote:
Dear gmx users,
I am new user of gromacs. Our calculations are
Dear Dr. Justin
Thank you for the insight . My problem is solved.
Best
Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State University
On Sat, Aug 9, 2014 at 5:00 AM,
gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
Send gromacs.org_gmx-users mailing list submissions
That's not what I said You can set...
-npme behaves the same whether or not GPUs are in use. Using separate ranks
for PME caters to trying to minimize the cost of the all-to-all
communication of the 3DFFT. That's still relevant when using GPUs, but if
separate PME ranks are used, any GPUs on
On Sat, Aug 9, 2014 at 4:52 AM, DASARI NAGARAJ dasarinagaraj...@gmail.com
wrote:
yes you can delete .trr files since they will not be of any use. they are
not useful during analysis also...
That depends on what the simulation is for, which Batdorj is best to judge
;-)
Mark
On Sat, Aug
Hi,
Gromacs is printing out WAYY more data then there is available on my small
cluster at UCSC. I just need position data from each simulation time step for
the analysis I want to perform. Is there a way that does not involve hacking
the source code to set mdrun to print out ONLY the *.xtc
On Sat, Aug 9, 2014 at 5:05 PM, Jackson Chief Elk jchief...@gmail.com
wrote:
Hi,
Gromacs is printing out WAYY more data then there is available on my small
cluster at UCSC. I just need position data from each simulation time step
for the analysis I want to perform. Is there a way that does
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