Hi user:
I was able to compile gromacs with GPU support without errors, but when I
test it with the benchmark got the following error:
(mdrun-gpu -device
OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no -s topol.tpr
-v)
Fatal error:
The selected GPU (#0, Tesla M2075) is not supported
Thanks!
On Tue, Oct 16, 2012 at 10:00 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/16/12 9:58 AM, Anthony Cruz Balberdi wrote:
Hi user:
I was able to compile gromacs with GPU support without errors, but when I
test it with the benchmark got the following error:
(mdrun-gpu -device
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
Hi Users:
I was trying to calculate the energy contribution of an specific ion in
my simulation. After extract a given frame from the simulation, I
recalculate
Thanks
On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
Hi Users:
I
Hi Users:
I was trying to calculate the energy contribution of an specific ion in my
simulation. After extract a given frame from the simulation, I recalculate
the energies of this frame with mdrun -rerun. Then I used tpbconv and
editconf to create a new gro file and a new tpr without the ion. I
Hi:
Did you add the parameters for the new covalent bond to the correct
part of ffbonded.itp? Because, for the GROMOS FF you have to add the
parameters for the new bond, angle and dihedral ,created due to
specbond, in a certain part of the ffbonded.itp for pdb2gmx be able to
use it. I dont know
Dear user:
I am planning to run some simulations of a protein encapsulated using
a rigid polymer but I not sure of what approach will be better. I was
thinking in using position restraint or freeze groups. Which procedure
will not cause problems or artifacts in the simulation? Any other idea
on
regards,
Anthony Cruz
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface
Dear Users:
We recently received our new computer. This computer have 4 multicore
Opteron AMD cpus and I am planning to install GROMAS. Which options I will
need to use in order to achieve the best possible performance?
Which compiler GNU or Intel?
Thank you for all you help.
Anthony
--
to link.
Mark
On Tue, Jul 5, 2011 at 10:26 AM, Matthew Zwiermczw...@gmail.com wrote:
Hi Anthony,
The default options are nearly optimal, and the difference between a
modern (4.4 or 4.5) GCC
On Tue, Jul 5, 2011 at 10:01 AM, Anthony Cruz Balberdi
anthony.cr...@upr.edu wrote:
Dear
Dear Yuvraj:
There is a protocol to find the charges and force field parameters for
new molecules for the AMBER force field. The best way is to try to
find the parameters from a publication. If you dont find anything then
use RED to find the charges (http://q4md-forcefieldtools.org/RED/).
Then
15:32, Anthony Cruz Balberdi anthony.cr...@upr.edu
wrote:
Dear Users:
I am interested in perform a simulation of a protein in different salt
concentrations. How I can calculate how much Na+ and Cl- ions to
include in the simulation to achieve certain concentration? Could
someone point me
Dear Users:
I am interested in perform a simulation of a protein in different salt
concentrations. How I can calculate how much Na+ and Cl- ions to
include in the simulation to achieve certain concentration? Could
someone point me in the right direction? Is there a software to do
this type of
I did it for other solvent. If you have AMBER is very easy to do. Do
you have AMBER?
On Wed, May 19, 2010 at 12:15 PM, vedat durmaz dur...@zib.de wrote:
hi all together,
this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent and using ffamber99 as force field. on
The mac computer is a cluster or just your personal computer?
If you will use it to prepare the system and for analysis you could
use macport or fink to compile gromacs.
Anthony
On Tue, May 11, 2010 at 11:13 AM, Emily Curtis
emilymariecur...@gmail.com wrote:
Dr. Bonner,
I am trying to install
google
for gromacs intel.
Best regards
Anthony
On Wed, May 5, 2010 at 7:25 PM, Anthony Cruz Balberdi
anthony.cr...@upr.edu wrote:
Sorry for my bad english... That happens to me but in linux. If you are using
mkl = 10 you need to change the way the libraries are called. Search
Here in the gromacs user contribution:
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software
I use it once.
Anthony
On Thu, Nov 12, 2009 at 7:49 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
ms wrote:
Hi,
I wonder if there is an easy way I am
Other way to do it is to edit the spectbond.dat for serach the atoms that
you want to bond. The same way that gromacs made the bond between the HEME
and the HIS
On Mon, Jul 13, 2009 at 6:27 PM, Jarol E. Molina hamolin...@gmail.comwrote:
Hi all
I need some monomers get bonds among them, but
I think that you can do it in vmd
On Tue, Jul 7, 2009 at 11:18 PM, Ragnarok sdf fabrac...@gmail.com wrote:
I came across a tool for making porcupine plots out of my PCA
analysis, but first I need to perform the analysis with a program that
accepts .cdr (amber traj) file format (the name of
to a
developer).
Cheers,
Tsjerk
On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz [EMAIL PROTECTED] wrote:
Hi users:
Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I
make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the
sasa analysis I observe differences
Hi users:
Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make
the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa
analysis I observe differences in the sasa values between the two versions.
The total sasa seems to be same in the two graphs but the
Dear Users:
I am planing to do some simulations of a protein in acetonitrile using the
model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model
will introduce new atom types and new LJ parameters for those atoms. When I
define those atoms in the acetonitrile topology I need to
Thank you for your rapidly responce David. If I use thr Gromos96 (ff43a1) it
will do it? How I check if the force field allows mixing?
Cheers,
Anthony
On Thursday 28 August 2008 01:34:30 pm David van der Spoel wrote:
Anthony Cruz wrote:
Dear Users:
I am planing to do some simulations
Hi User:
We have a protein with two domains. This two domains were connected by two
linkers of different length. We want to study the different conformation that
the protein domains can adopt depending the length of the linkers without
loosing the secondary structure feature present. I was
Hi User:
We have a protein with two domains. This two domains were connected by two
linkers of different length. We want to study the different conformation that
the protein domains can adopt depending the length of the linkers without
loosing the secondary structure feature present. I was
Hi users:
I am working in a new projec and we plan to do some molecular dynamic
experiment to an engineered GFP molecule. I have been searching for the
parameters for the GFP chromophore without success. Can some one help me? Any
reference or parameters??
Best Regards,
Anthony
important for debugging. If you don't know it
doesn't apply to you :-)
All that matters for you is that 3.3 = 3.2, so it should work fine;
the hardware doesn't matter.
Cheers,
Erik
On Aug 8, 2007, at 12:25 AM, Anthony Cruz wrote:
Hi Erick,
Thank you for you responce. I am sorry but I dont
on architectures where
we use tuned assembly loops.
Cheers,
Erik
On Aug 7, 2007, at 10:57 PM, Anthony Cruz wrote:
Hi users:
I have made some simulation in one of our workstation. Now I want
to extend
the simulations few nanoseconds. I can continue the simulations in
other
machine without
Hi:
I am running a simulation (on GROMACS 3.3.1) were I want to save the
coordinates of a group of atoms every steep. I
use the nstxtcout and xtc_grps options in my MDP file. The problem is that when
I continue the simulation (using
tpbconv -f -e -s -until) the first 100 to 500 ps the
Hi Ozge:
You can use a script in VMD to do the work. In VMD you could make various atom
selection and use it in the script. You
could use something like this:
set outfile [open sol_within_prot.dat w];
set nf [molinfo top get numframes]
set frame0 [atomselect top protein frame 0]
# water
Hi Jochen:
Did you receive any responce??? I font 2 different parameters for NO. one of
2 sites and other of three sites. I try to build the three sithe model but I
can get it to work because I have problems with the third site, a dummy atom.
Probably you have more experience with GROMACS than
Hi Users:
I have a question about dummy atoms. I try to simulate a protein that have a
cysteine modified with a NO group. I found a NO model that have 3 sites, one
at each atom and other in the center of mass (Biophys. Chem. 98 (2002) 183).
[ SNC ]
[ atoms ]
N N-0.28000 0
Hi user:
Today I have been working with a heme protein and I notice that in the topology
the parameters that include the His
(NE2) and the heme (FE) were not present in the topology (bon type, angle type,
etc). Also when I check the topology
after grompp (-pp) this file also do not include
Hi User:
I have a little question about the LJ parameters. If I download a molecular
topology from the site or build a new
molecule from parameters in the literature that have new atom types with new LJ
parameters, how the combinations of LJ
parameters will be done between this new LJ and the
Hi User:
I have a little question about the LJ parameters. If I download a molecular
topology from the site that have new atom
types with new LJ parameters, I supposed to add an [ atomtypes ] section to the
topology that define the new types and
the new LJ. The question is I need to add the
HI Users:
I want to rerun my system to determine the energy of the protein. What I need
to do?
If the answer is to set up energygrp_excl I could include all the component of
the system except the protein in one
group an use this group for the energygrp_excl because my system have 6
Hi users:
I have a little question. I found some L-J parameters for heme iron for the
GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear
in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5
and B (kJ nm^ -6 mol ^ -1) 8.886909e-3. I need to make
Hi:
I have been trying to made a solvent box of methacrylic acid using parameters
from PRODRG. I change it to GROMOS96 parameters and use charges from DFT
calculation. I do the energy minimization with out any problem. I run a 2ns
MD (NVT) with out any problem too. But when I try to run an MD
What procedure will be better? Freeze or position restrain?
Anthony
On Monday 01 May 2006 7:17 am, Anthony Cruz wrote:
On Friday 28 April 2006 12:02 pm, David van der Spoel wrote:
Anthony Cruz wrote:
Hi:
I want to make a simulation of a small pepetide in a box of water but I
want
Hi:
I have been trying to make the manual from cvs and I can make it. If someone
have it please could send me a copy ???
Thanks
Anthony
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't
40 matches
Mail list logo