Hey guys,
Meanwhile I run my simulations on a CUDA card and must say that I am very
very satisfied with it.
Nevertheless I have a few questions regarding to a improved performance:
1. Is it possible to perform the PME calculation on the CUDA card? I always
see in md.log that the PME runs on the
Respected sir,
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P.
On 9/3/13 7:20 AM, Prajisha Sujaya wrote:
Respected sir,
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96
Dear Gmx Users,
i wish I could restrain some ions in my system (NA). I tried to include it
in ions.itp:
[ moleculetype ]
; molnamenrexcl
NA1
#ifdef POSRES_NA
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
#endif
But it does not work.
Hello all,
A Quick question below:
My peptide contains one trp, and i want to select only the atoms that form the
the indol ring. I would like a portable script for others systems that contain
also a peptide with one Trp residue. So I am not interesting to select the
corresponding atoms by
On 9/3/13 8:14 AM, Steven Neumann wrote:
Dear Gmx Users,
i wish I could restrain some ions in my system (NA). I tried to include it
in ions.itp:
[ moleculetype ]
; molnamenrexcl
NA1
#ifdef POSRES_NA
[ position_restraints ]
; atom type fx fy fz
1 1 1000
On 9/3/13 8:57 AM, ABEL Stephane 175950 wrote:
Hello all,
A Quick question below:
My peptide contains one trp, and i want to select only the atoms that form the
the indol ring. I would like a portable script for others systems that contain
also a peptide with one Trp residue. So I am not
Dear all,
I am just starting MD simulations and wanted to see how to perform steered
molecular dynamics in gromacs . Most papers and tutorials that I found were
done in NAMD. Can anyone recommend examples that were done in gromacs? In my
case the tutorial Pull Code and Umbrella Sampling
On 9/3/13 11:36 AM, ABEL Stephane 175950 wrote:
Hello Justin,
My question was How to select the following atoms CG, CD1, HD1, CD2, CE3, HE3, CZ3,
HZ3, CH2, etc.. present ONLY in the trp residue with a single line command with
make_ndx. Indeed some of them can be also present in other
On Tue, Sep 3, 2013 at 9:37 AM, grita cemilyi...@arcor.de wrote:
Hey guys,
Meanwhile I run my simulations on a CUDA card and must say that I am very
very satisfied with it.
Nevertheless I have a few questions regarding to a improved performance:
1. Is it possible to perform the PME
On 9/3/13 11:22 AM, hanna pdb wrote:
Dear all,
I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in
gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples
that were done in gromacs? In my case the
Hello Justin,
My question was How to select the following atoms CG, CD1, HD1, CD2, CE3,
HE3, CZ3, HZ3, CH2, etc.. present ONLY in the trp residue with a single line
command with make_ndx. Indeed some of them can be also present in other
residues.
Stephane
--
Hi Mark,
1e-9 is indeed an abnormally high tolerance to use, I was just testing
higher precisions to see if I can get better energy conservation.
I ran some 1ns tests with different tolerances and compared avx and sse
instruction sets. I'm still seeing a discrepancy between the two
instruction
On Tue, Sep 3, 2013 at 6:17 PM, Ali Sinan Saglam asinansag...@gmail.com wrote:
Hi Mark,
1e-9 is indeed an abnormally high tolerance to use, I was just testing
higher precisions to see if I can get better energy conservation.
Did you read all of what manual section 7.3 has to say about the
Dear GMX users,
I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver
11.x). Here is how I compiled FFTW,
./configure CC=icc F77=ifort CFLAGS=-O3 -gcc
--prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads
--enable-sse2 --with-combined-threads
Hi Dear Gromacs users,
I would like to calculate the standard deviation (as the error bar) for
dV/dlambda.xvg file. I used g_analyze command as the following:
g_analyze -ffree0.9.xvg -av average_0.9
I got:
set average*standard deviation**std. dev. /
Hi all,
I've written a tool, called psf2top.py which can convert NAMD PSF files
directly to GROMACS topologies. It is part of PyTopol package and is available
here https://github.com/resal81/PyTopol .
Please note that PyTopol is currently in alpha stage. If you test psf2top.py on
your PSF
On 9/3/13 1:47 PM, Guanglei Cui wrote:
Dear GMX users,
I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver
11.x). Here is how I compiled FFTW,
./configure CC=icc F77=ifort CFLAGS=-O3 -gcc
--prefix=/tmp/gromacs-4.6.3/fftw-3.3.3/build-intel-threads --enable-threads
Hi Justin,
Thanks for the response. Right now, I will just have to get around this by
using a slower code. How do I switch off SSE4.1 and use a different CPU
optimization scheme?
Regards,
Guanglei
On Tue, Sep 3, 2013 at 2:39 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/3/13 1:47 PM,
Also, why in vacuo? At least turn on an implicit solvent model.
Gianluca
On Tue, 3 Sep 2013, Justin Lemkul wrote:
On 9/3/13 11:22 AM, hanna pdb wrote:
Dear all,
I am just starting MD simulations and wanted to see how to perform steered
molecular dynamics in gromacs . Most papers and
Hi Mark,
I agree with you and Justin, but let's just say there are things that are
out of my control ;-) I just tried SSE2 and NONE. Both failed the
regression check. I think I've spent enough time on this, which justifies
escalating this to someone with the control, but is failing regression
Can't be sure - we don't know what the problem with the compiler *is*.
Mark
On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui
amber.mail.arch...@gmail.com wrote:
Hi Mark,
I agree with you and Justin, but let's just say there are things that are
out of my control ;-) I just tried SSE2 and NONE.
On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui
amber.mail.arch...@gmail.com wrote:
Hi Mark,
I agree with you and Justin, but let's just say there are things that are
out of my control ;-) I just tried SSE2 and NONE. Both failed the
regression check.
That's alarming, with
On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui
amber.mail.arch...@gmail.com wrote:
Dear GMX users,
I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver
11.x). Here is how I compiled FFTW,
./configure CC=icc F77=ifort CFLAGS=-O3 -gcc
On 9/3/13 3:10 PM, Gianluca Interlandi wrote:
Also, why in vacuo? At least turn on an implicit solvent model.
I can think of reasons to study molecular interactions in vacuo via pulling.
Why is solvent (explicit or implicit) an absolute requirement?
-Justin
On Tue, 3 Sep 2013, Justin
Hello
I am running a simulation with charge and without charge for 128 pairs of
bmim-tf2n ioinc liquids.
This is the command for the original run without charge
mdrun -s gs.tpr -o gs.trr -c 0.pdb -e gs.edr -g gs.log -pd -nt 8
This is the command for the rerun with charge
mdrun -s es.tpr -o es.trr
On 9/3/13 3:10 PM, Gianluca Interlandi wrote:
Also, why in vacuo? At least turn on an implicit solvent model.
I can think of reasons to study molecular interactions in vacuo via pulling.
I'm sure there are.
G
Why is solvent (explicit or implicit) an absolute requirement?
-Justin
On
On 9/2/13 9:43 PM, Jernej Zidar wrote:
Dear Justin,
I set the couple_intramol parameter to yes and rerun the free energy
simulations. mdrun was able to fully utilize all the cores in the
system but there's one issue. The free energy of solvation is vastly
different if the parameter is set
Dear all,
Can anyone please share your heme ligated to CO ligand parameters? There is a
parameters file exist in charmm22 and gromos but they are not well defined.
It would be really appreciated if you anyone share here. Thanks.
--
gmx-users mailing listgmx-users@gromacs.org
Hi Szilard,
Thanks for your reply. I may try your suggestions tomorrow when I get back
to work.
Feeling curious, I downloaded and compiled gmx 4.6.3 on my home computer
(gcc-4.6.3 and ubuntu 12.04). Even with the default (below), kernel (38 out
of 142) and freeenergy (2 out of 9) tests would
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