See http://redmine.gromacs.org/issues/1471
/Anders
On 25 Apr 2014, at 19:55, Stephen N. Floor fl...@berkeley.edu wrote:
Hi and thanks -
I did end up ignoring the warning about no compatible GPUs. The non-openmp
compiler went away once I finally convinced cmake to actually use gcc-4.8.2
dear Mr.alizadeh
thanks for your reply
the repeatability of average pressure is my problem. average pressure isn't
repeatability
when i repeat NPT simulation stage many times, simulation results are very
different for the pressure average.
my system is protein-ligand complex. How long do you
dear Mr.alizadeh
thanks for your reply
my problem hasn't good repeatability.
when i repeat NPT simulation stage many times, simulation results are very
different for the pressure average.
my system is protein-ligand complex. How long do you think is enough for the
NPT stage?
Regards
On Monday,
Dear Mahboobe,
I do not know what exactly you mean. You know what, I do not know which
your target system is. I mean when you want to simulate a system you should
know which thermostat
you need. Generally In mailing lists(as I always make some mistake) anyone
knows any details of your system. I
On 4/28/14, 12:04 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:
Dear gromacs users,
I am doing a protein-peptide interaction...
when I do NVT (300K) and NPT (1bar) for 200 ps I get the following results
using g_energy
Temp. 299.8 K
Pressure- -1.7bar
Should I go ahead
On 4/28/14, 1:37 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:
Dear Gromacs user,
After I give the command for nvt, I get the following error:
starting mdrun 'Protein in water'
15 steps,300.0 ps.
Step 0, time 0 (ps) LINCS WARNING
If the run crashes at step zero, it
dear justin
Thank you sincerely.
I wish you the best.
Regards
mahboobeh
On Monday, April 28, 2014 2:48 PM, Justin Lemkul jalem...@vt.edu wrote:
Please keep the discussion on the list. I can see from the other posts that
providing this information to everyone likely would have been
Hi,
I'm using tabulated potentials to create a hole in a membrane. I define
three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For
the interactions between the dummy atoms and the hydrophobic chains I
define an exclusively repulsive potential. All other interactions are
Dear gromacs users,
I have a problem regarding the simulation of Azurin protein attached to
metal atom of
Cu. I edited the aminoacids.rtp file including CU as residue and i added
the type of covalent bond that i need in the terminal part of ffbonded.it
that regard special bonds.
I have
On 4/28/14, 9:14 AM, Alessia Giuliani wrote:
Dear gromacs users,
I have a problem regarding the simulation of Azurin protein attached to
metal atom of
Cu. I edited the aminoacids.rtp file including CU as residue and i added
the type of covalent bond that i need in the terminal part of
On 4/28/14, 9:19 AM, Sabine Reisser wrote:
Hi,
I'm using tabulated potentials to create a hole in a membrane. I define three
groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the
interactions between the dummy atoms and the hydrophobic chains I define an
exclusively repulsive
On 4/28/14, 10:15 AM, fantaman wrote:
Dear GROMACS users,
if I want to define a new bond, should I define it in the [ bonds ] section
of the corresponding [ aminoacid ] section in top/aminoacid.rtp or should I
leave this section (I mean [ bonds ]) empty and introduce the bond in the
file
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