Hello,
I was able to generate .str file from CGenFF server, and after this, i am
able to convert the .str files into .itp, .prm files etc., successfully by
using the cgennff_charmm2gmx.py script. but at the end, i am getting the
notes as:-
NOTE1: Code tested with python 2.7.3. Your version: 2.7.1
Hi,
It's not only the core count that matters, the speed of the cores also
does! For that reason, the high-clock Intel i9 and Threadripper CPUs
will be often faster than many dual socket machines with more cores.
BTW, servethehome.com has recently started doing benchmarks with
GROMACS and has ill
On 10/17/17 2:03 PM, Dilip H N wrote:
Hello,
1] I want to run simulations using charmm 36 FF in gromacs, will it be
compatible with charmm 36 FF ..??
2] How does it asses the molecule naming since in each force field the
atoms of the molecules may be named differently...
Any suggestions...
Hi,
I am adding a Mg2+ Dummy model to the AMBERff03 FF in GROMACS 2016.3,using the
paramters from Jiang et al. (given in the supporting material)
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00286as the newest and "most
reliable for ATP-Mg2+-Protein conformations".
I was able to implement al
Hello,
1] I want to run simulations using charmm 36 FF in gromacs, will it be
compatible with charmm 36 FF ..??
2] How does it asses the molecule naming since in each force field the
atoms of the molecules may be named differently...
Any suggestions...
Thank you.
--
With Best Regards,
DILIP
Please, get it here
svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
acpype
Interestingly, but Google code still holds the correct information too:
https://code.google.com/archive/p/acpype/
On 17 October 2017 at 16:19, Easton J.W. wrote:
> Dear Maud
On Sun, Oct 15, 2017 at 3:13 PM, Deron Johnson wrote:
> BTW: I’m using
>
> gromacs 5.1.4
> VMD 1.9.3
>
> on a Macbook Pro with macOS 10.12.3 (Sierra).
>
> > On Oct 15, 2017, at 12:08 PM, Deron Johnson wrote:
> >
> > I am new to gromacs. I followed the steps of the lysozyme tutorial
> > (http://w
BTW: I’m using
gromacs 5.1.4
VMD 1.9.3
on a Macbook Pro with macOS 10.12.3 (Sierra).
> On Oct 15, 2017, at 12:08 PM, Deron Johnson wrote:
>
> I am new to gromacs. I followed the steps of the lysozyme tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/0
Dear Maud,
Thanks, I will give that a try,
Regards,
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Maud Jusot
Sent: 17 October 2017 16:10:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Creating cyclic peptides
Dear Jame
Dear James,
If you want to use an Amber force field, you can create the topology in
the amber format with AmberTool and then convert it to the gromacs
format using Acpype tool
(http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder). It works for
cyclic peptides.
Best regards,
Maud
Le 1
Thanks Justin,
Is there anyway of getting it to work using an AMBER forcefield as well?
Kind regards,
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 17 October 2017 15:46:27
To: gmx-us...@gromacs.org
Subject
On 10/17/17 10:13 AM, Easton J.W. wrote:
Hi,
I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to
do this using either an AMBER or CHARMM forcefield.
Initially I have been following the instructions in this link,
https://mailman-1.sys.kth.se/pipermail/gromacs.org
On Tue, Oct 17, 2017 at 8:05 AM, Giuseppe Léonardo Licari <
giuseppe.lic...@unige.ch> wrote:
> Dear all,
>
> I have troubles with umbrella sampling. During the umbrella sampling
> simulation the COM distance between the two solutes is going too far from
> the set initial value. I tried to increase
Hi,
I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to
do this using either an AMBER or CHARMM forcefield.
Initially I have been following the instructions in this link,
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html
Howev
Dear all,
I have troubles with umbrella sampling. During the umbrella sampling simulation
the COM distance between the two solutes is going too far from the set initial
value. I tried to increase a lot the force constant of the harmonic potential.
I also tried to change "umbrella" to "contraint
Hi all,
I have a very basic question about essential dynamics. I want to know
whether essential dynamics function is similar to Accelerated MD ? Or
essential dynamics is different from Accelerated MD ?
Thanks in advance.
Kingsleg Theras
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Gromacs Users mailing list
* Please search the archive
BS”D
On 17 Oct 2017, at 1:03 PM, Bernhard Reuter
mailto:b.reu...@uni-kassel.de>> wrote:
Dear Harry,
I would assume you are right with your argument that 6/8/10 cores per GPU are
better than i.e. 5 cores. If I were you I would still carefully test, if you
really have a big performance gain wi
Hi,
CUDA 9.0 doesn't support that ancient architecture, but old GROMACS code
didn't know that would happen. Either use an older CUDA or a newer GROMACS,
e.g. 2016.4.
Mark
On Tue, Oct 17, 2017 at 11:34 AM Chetan Puri wrote:
> I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40
>
Dear Harry,
I would assume you are right with your argument that 6/8/10 cores per
GPU are better than i.e. 5 cores. If I were you I would still carefully
test, if you really have a big performance gain with a i9 16 core and
two vs. one GPU. There are two reasons for this: 1. The 1080ti is
sig
I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40
But on the make step I am getting error
nvcc fatal : unsupported gpu architecture 'compute_20'
So can anyone suggest how to resolve it.
CHETAN
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Su
BS”D
Dear Bernhard and Szilárd,
Since your replies to me are related, I’ll combine my replies to one letter.
you are right for the dual xeon 16 core setup you (and we) use, but for the
single core i9 setup we made the experience, that we only gained between 5-10%
of performance by adding a sec
Hi,
Force is a vector, yes. And its units are not kcal/mol nm in GROMACS. See
chapter 2 of the reference manual.
Mark
On Tue, Oct 17, 2017 at 9:00 AM Chang Woon Jang
wrote:
> Dear Justin,
>
> Thank you for your help. One more question is that there are positive
> and negative values. Does
Hi,
That's your question as part of your experimental design. Why do you want
to do simulated annealing?
Mark
On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash
wrote:
> Is simulated annealing carried out during NPT or in the production run?
>
> Akash
>
> -Original Message-
> From: gromacs
Is simulated annealing carried out during NPT or in the production run?
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: 20 September 2017 03:20
To: gmx-us...@gro
Dear Justin,
Thank you for your help. One more question is that there are positive
and negative values. Does this mean that the forces are written as
vector values? For example, the value of -40 means negative Z direction
with 40 kcal/mol nm ?
Thank you.
Best regards,
Changwoon Jang
On Mon,
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