--
Carmen Di Giovanni, PhD
Dept. of Pharmaceutical and Toxicological Chemistry
Drug Discovery Lab
University of Naples Federico II
Via D. Montesano, 49
80131 Naples
Tel.: ++39 081 678623
Fax: ++39 081 678100
Email: cdigi...@unina.it
Hi Szilard,
I post also the output of the command:
gmx_mpi
Dear Szilárd,
1) the output of command nvidia-smi -ac 2600,758 is
[root@localhost test_gpu]# nvidia-smi -ac 2600,758
Applications clocks set to (MEM 2600, SM 758) for GPU :03:00.0
Warning: persistence mode is disabled on this device. This settings
will go back to default as soon as driver
Dear Szilárd,
1) the output of command nvidia-smi -ac 2600,758 is
[root@localhost test_gpu]# nvidia-smi -ac 2600,758
Applications clocks set to (MEM 2600, SM 758) for GPU :03:00.0
Warning: persistence mode is disabled on this device. This settings
will go back to default as soon as
Hi, I tried using charmm forcefield to simulate heme but we are getting
warning messages.
WARNING: atom HA is missing in residue HEME 1500 in the pdb file
.
.
.
for all 30 hydrogens.
Later we tried modifying the aminoacids.hdb as:
HEME3
1 5 HA CA N C CB
1
On 2/18/15 11:13 PM, Sanchaita Rajkhowa wrote:
Dear Justin, thank you for the reply. However, I would like to know if
there is any server which can generate parameters for heme to be used in
OPLS-aa? We have already tried in swissparam with failed results. Please
help.
I have no idea if
On 2/19/15 2:21 AM, Meena Singh wrote:
Dear GROMACS users,
I am trying to simulate box of 1-ethyl-3-methylimidazolium ion (5-membered
ring with overall +1 charge) with its counter ion tetrafluoroborate.
I am using OPLS forcefield.
Partial charges and potential parameters have been taken from
On 2/19/15 12:59 AM, Antara mazumdar wrote:
Hi,
I am trying to simulate a peripheral membrane protein in a heterogenous
lipid bilayer of DOPC and DOPG using charmm 36 force field in GROMACS. i
need mdp files for NPT, NVT, steep and MD to check whether the conditions i
am using to simulate my
Dear all,
How is the situation with this issue?
http://redmine.gromacs.org/issues/667
I am planning to modify this function to look for the fastest oscillations
in each system and that is why I am asking this question.
Thank you very much.
Best regards,
Mario
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Gromacs Users mailing list
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On Feb 19, 2015, at 9:49 AM, Zahra Ghanbari, zahraghanbar...@gmail.com
wrote:
hi
I installed topolbuild version 1.3. I used following command line:
./topolbuild -dir /home/supermicro/topolbuild1_3/dat/gromacs -ff oplsaa -n
OXL -r OXL -meas -rename -move
I encountered with following error:
On Feb 19, 2015, at 12:44 PM, Zahra Ghanbari zahraghanbar...@gmail.com wrote:
Dear Ray
I tried to use another .mol2 file. I use USCF chimera to save it.
@TRIPOSMOLECULE
OXL.pdb
6 5 1 0 0
SMALL
NO_CHARGES
@TRIPOSATOM
1 C1 47.7640 52.0960 49.3000 C.2 1 OXL0.
On 2/19/15 12:55 PM, virginia miguel wrote:
Hi everyone; I am tryingto run a simulation of a DNA-protein complex obtained
by docking of a dsDNA of18bp to a crystal structure of the recA protein using
GPU. I used amber ff, adodecahedron cell with 15A of distance from the surface
of the
Dear Users
This is my earlier post wherein I received useful suggestion from Dr.
Lemkul.
http://comments.gmane.org/gmane.science.biology.gromacs.user/74659
Earlier for my system , I was doing a 1 ns Umbrella Sampling run for each
window and my histogram looked like this :-
HISTO
Dear Ray
I tried to use another .mol2 file. I use USCF chimera to save it.
@TRIPOSMOLECULE
OXL.pdb
6 5 1 0 0
SMALL
NO_CHARGES
@TRIPOSATOM
1 C1 47.7640 52.0960 49.3000 C.2 1 OXL0.
2 C2 48.9620 53.0060 49.8530 C.2 1 OXL0.
3 O1
Thanks Justin. It was the merging of the hbonds data that led to show the
repetition of the list. If we do nomerge everything is reasonable.
On Wed, Feb 18, 2015 at 7:41 AM, Justin Lemkul jalem...@vt.edu wrote:
On 2/17/15 5:14 PM, Udaya Dahal wrote:
Thanks Justin for prompt reply. Actually
On Thu, Feb 19, 2015 at 11:32 AM, Carmen Di Giovanni cdigi...@unina.it wrote:
Dear Szilárd,
1) the output of command nvidia-smi -ac 2600,758 is
[root@localhost test_gpu]# nvidia-smi -ac 2600,758
Applications clocks set to (MEM 2600, SM 758) for GPU :03:00.0
Warning: persistence mode is
Szilard,
about:
Fatal error
1) Setting the number of thread-MPI threads is only supported with thread-MPI
and Gromacs was compiled without thread-MPI
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Hi everyone; I am tryingto run a simulation of a DNA-protein complex obtained
by docking of a dsDNA of18bp to a crystal structure of the recA protein using
GPU. I used amber ff, adodecahedron cell with 15A of distance from the surface
of the complex and neutralizedwith counter ions (42 NA+,
Please consult the manual an wiki.
--
Szilárd
On Thu, Feb 19, 2015 at 6:44 PM, Carmen Di Giovanni cdigi...@unina.it wrote:
Szilard,
about:
Fatal error
1) Setting the number of thread-MPI threads is only supported with
thread-MPI
and Gromacs was compiled without thread-MPI
For more
Hi,
Nothing has happened.
Mark
On Thu, Feb 19, 2015 at 4:31 PM, Mario Fernández Pendás mariof...@gmail.com
wrote:
Dear all,
How is the situation with this issue?
http://redmine.gromacs.org/issues/667
I am planning to modify this function to look for the fastest oscillations
in each
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