W dniu 22.09.2014 o 16:45, Александр Селютин pisze:
Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2 ps.
But it can be very slowly. Does anybody know how to do it more correctly?
Dear users,
Can we calculate electrostatic energy between two groups of atoms in
GROMACS?
Best wishes,
H.A
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I used the command mdrun_mpi -v -deffnm test to run the .tpr file and find
some new information in my log file:
GPU timings
-
Computing: Count Wall t (s) ms/step %
Dear all,
Short and fast: I'm interested in using/testing the TIGER2*** method,
currently implemented in NAMD, but I'm what you would call a GROMACS
person. Are there any plans to implement it for GROMACS in the near
future? Is this something that has been discussed among the developers at
some
On 9/23/14 7:36 AM, h.aliza...@znu.ac.ir wrote:
Dear users,
Can we calculate electrostatic energy between two groups of atoms in
GROMACS?
energygrps in the .mdp file.
Whether or not that quantity means anything (if using PME, for instance) is
another matter and depends to some extent on
Hi,
I don't know of anyone with such plans. It wouldn't be hard for the right
person, but that goes for dozens of things such a person could do... :-)
Mark
On Tue, Sep 23, 2014 at 1:46 PM, João Henriques
joao.henriques.32...@gmail.com wrote:
Dear all,
Short and fast: I'm interested in
Ok, I see what you mean. Thanks anyway.
Best regards,
João
On Tue, Sep 23, 2014 at 1:49 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
I don't know of anyone with such plans. It wouldn't be hard for the right
person, but that goes for dozens of things such a person could do... :-)
I guess you'll have to become a NAMD person ;-)
On Tue, Sep 23, 2014 at 2:22 PM, João Henriques
joao.henriques.32...@gmail.com wrote:
Ok, I see what you mean. Thanks anyway.
Best regards,
João
On Tue, Sep 23, 2014 at 1:49 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
I
hi all,
why cannot g_dos accept -n as supposed?
and g_dos normally gives very sharp curve, any thoughts on that?
P.S. I use 2 fs to integrate a typical protein-water system.
Thanks,
Yao
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Hi.
On stampede of xsede.org https://portal.xsede.org/tacc-stampede, I
compiled cmake, and then gromacs 4.6.7 with and without gpu, with the
following cmake configuration:
without gpu:
module load mkl
module load cuda/6.0
module load mvapich2
export MKLROOT=$TACC_MKL_DIR
export
On 9/23/14 12:45 PM, Johnny Lu wrote:
Hi.
On stampede of xsede.org https://portal.xsede.org/tacc-stampede, I
compiled cmake, and then gromacs 4.6.7 with and without gpu, with the
following cmake configuration:
without gpu:
module load mkl
module load cuda/6.0
module load mvapich2
export
Hello all,
I am trying to convert some GLYCAM parameters to do simulations with the
GROMACS code. In the glycam force field, several dihedral terms have negative
barrier height values, for instance, -20 in the following parameter:
Os-Cj-Cj-Ha 1 -20.00 0.0 2
Can I ask you something. What do you mean by rolled up? Do you mean create
the tangled conformation of polymer chains?
--Farid
22.09.2014, 20:46, marcello cammarata mstaxmarce...@yahoo.it:
Hi,
i had checked all the archives, i have read about 100posts in the last 2
month.
Nobody have
On 9/23/14 1:18 PM, ABEL Stephane 175950 wrote:
Hello all,
I am trying to convert some GLYCAM parameters to do simulations with the
GROMACS code. In the glycam force field, several dihedral terms have negative
barrier height values, for instance, -20 in the following parameter:
yes,
i need yto know how it go to tangled, related with the lenght of chain, the
number of chains in volume unit.
For now the problem is that when i run pdd2gmx, i don't choose any solvent,
because there isn't eny solvent, i choose only a kind of force field present in
the database software.
hi all,
I wonder why g_dos cannot accept -n as supposed?
and why g_dos normally gives very sharp curve, any thoughts on that?
P.S. I use 2 fs to integrate a typical protein-water system.
Thanks,
Yao
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It works now. I didn't know there are gpudev and gpu queues. Have to
use those to run cuda programs.
There are 3 gpu per node...
i loaded the correct intel version and then the one without cuda ran ok.
On Tue, Sep 23, 2014 at 1:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/23/14 12:45
Do you know how change force field?
how i can do this?
so the goal can be this, i can consider two molecules asmetilene or ethilene or
butene, and i want kwon by appling a set of force field the mutual distance
beetween the two groups.
How i can do this?
how is possible to set force field?
Hi,
I've been working with GLYCAM parameters in Gromacs by converting them into
Gromacs format using Acpype: https://code.google.com/p/acpype/ . I haven't
compared the single-point energy with Amber, but the Gromacs-formatted
output is perfectly usable.
Regards,
Tamir
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On 9/23/14 7:43 PM, marcello cammarata wrote:
Do you know how change force field?
how i can do this?
Everything you need to create the polymer is described here:
http://www.gromacs.org/Documentation/How-tos/Polymers
The page includes a link to a discussion that goes step-by-step through
Try -nt, -ntmpi, -ntomp, -np (one at a time) ?
I forget about what I tried now But I just stop the mdrun, and then
read the log file.
Also can look for the mdrun page in the offical manual (pdf) and try this
page:
http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun?highlight=mdrun
hi. can i get a link to the redmine issue?
I decided to install 4.6.7 instead of 5.0.1 because of this.
On Mon, Sep 22, 2014 at 5:52 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Mon, Sep 22, 2014 at 11:02 AM, Machtens, Jan-Philipp
j.macht...@fz-juelich.de wrote:
Thanks for the
I used the command mdrun_mpi -v -deffnm test to run the .tpr file and find
some new information in my log file:
GPU timings
-
Computing: Count Wall t (s) ms/step %
I think that the items (wait GPU nonlocal) and (wait GPU local) in log file are
the time consuming that cpu wait for gpu. And Does anyone know that which item
is the time consuming that gpu wait for cpu in log file?
xiexiao...@sjtu.edu.cn
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Thank you Lu for the reply.
As I have mentioned in the post, I have already tried those options but it
didn't work. Kindly please let me know if you have anymore suggestions.
Thank you,
On Tue, Sep 23, 2014 at 8:41 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Try -nt, -ntmpi, -ntomp, -np (one
Hi Gromacs users,
When I do msd analysis (g_msd), there is a promotion to select a group number.
I am wondering how can I select a number using a script. So the computer can
do analysis automatically.
Thank you.
_
Xiaobin Cao
Dept of Geology
Use echo
$echo 0 | g_msd -s topol.tpr -f traj.xtc
Chandan
On Wed, Sep 24, 2014 at 9:35 AM, Xiaobin Cao x...@lsu.edu wrote:
Hi Gromacs users,
When I do msd analysis (g_msd), there is a promotion to select a group
number. I am wondering how can I select a number using a script. So the
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