for
example)?
Are there any tutorials?
Thanks in advance,
Hovakim Grabski
Russia- Armenian(Slavonic) University
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Dear Gromacs users,
Is it possible to use GROMACS 4.6 GPU Mode on Nvidia 250 GTS?
Thanks in advance,
Hovakim
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topology
#include ETA.itp
Is there any way to fix it?
Thanks in advance,
Best regards,
Hovakim Grabski
Russian-Armenian(Slavonic) University
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Grabski hovakim_grab...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Отправлено: четверг, 29 ноября 2012 16:24
Тема: Re: [gmx-users] Hbonds between Adenine and Thymine
Please keep the discussion on the gmx-users list.
On 11/29/12 6:12 AM, Hovakim Grabski wrote:
Dear Justin
can I select Adenine from one strand and Thymine from the other strand and
then run g_hbond ?
Thanks in Advance
Best regards,
Hovakim Grabski
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a sudden change.
Is there any chance I could see intercalation?
P.S. Or I should create an artifical gap between dna bases and then set up a
simulation?
Thanks in advance,
Best regards,
Hovakim Grabski--
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Dear Gromacs users,
I want to set up an umbrella sampling simulation of an Hypericin dimer.
I have created position restraint files for hypericin with genrestr and then
use it with the topology file, so I want to know if it is just restraining one
of the Hypericin Molecules or both of them?
Dear Gromacs users,
I set up a simulation of 4 Hypericin molecules for 5 ns.
2 of them formed a dimer.
Is there any way to find the dissociation constant Kd and bond energy of
Hypericin ?
Thanks in advance
Hovakim--
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Dear Gromacs users,
I set up a simulation between the DNA fragment and 6 podophyllotoxin
molecules, the topology files were generated with acpype, simulation time
was 2.8 nanoseconds, but the results are not what I expected. 4 molecules of
PTOX formed an aggregate and then formed hydrogen
Dear Gromacs users,
I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 of them
formed an aggregate.Is there any way to find out between what molecules and
atoms Hbonds were formed?
Thanks in advance
Hovakim Grabski
Russian-Armenian(Slavonic) University
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about 5400 kJ/mol and for the
second one is 28000 kJ/mol). I wonder if g_energy extracts the energy values
from the whole system including the water molecules,and if it is so is there
any way to extract the kinetic energy values of the Hypericin molecules?
Thanks in Advance
Hovakim Grabski
in Advance
Hovakim Grabski
Russian-Armenian(Slavonic) University--
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Dear GROMACS users,
I have been trying to set up a simulation system containing 4 Hypericin
molecules in a box of water.
When I'm trying to run energy minimization,I get this error:
WARNING 1 [file HYP1_GMX.itp, line 5]:
Overriding atomtype CT
WARNING 2 [file HYP1_GMX.itp, line 6]:
an index file linking the DNA and Hypercin into on
tc-grps and ran the simulation for 1 ns. Is it enough or it should run longer?
My PC is quadcore Q6600 with 2 gigs of ram.
Thanks in advance
Hovakim Grabski
Russian Armenian (Slavonic) University
Bionformatics Department--
gmx-users mailing list
Hi,
Anyone know any ligand- ligand tutorial?
I've been trying to set up a taurine simulation with lysophosphatidylcholines
(LPC) with no success.
Thanks in Advance--
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in Advance
Hovakim Grabski
Russian-Armenian Slavonic University--
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