Anamika Awasthi wrote:
Dear Xavier
Thanks for your help, after running my tpbconv I got this
Telling us the command line might be helpful!
Reading toplogy and shit from 2ao2_tpxout.tpr
Reading file 2ao2_tpxout.tpr, VERSION 3.3 (single precision)
READING COORDS, VELS AND BOX FROM TRAJECTORY
Dear Xavier
Thanks for your help, after running my tpbconv I got this
Reading toplogy and shit from 2ao2_tpxout.tpr
Reading file 2ao2_tpxout.tpr, VERSION 3.3 (single precision)
READING COORDS, VELS AND BOX FROM TRAJECTORY 2ao2_tpxout.trr...
trn version: GMX_trn_file (single precision)
Read fra
hi,
I am using tabulated van dar waals potential. In the table I have given
only g(x) and g''(x) and everything else as zeros. The system is LJ
molecules with no charge. And I have put a new atom type which has c6
and c12 = 1.0 and mass = 1.0. Is this OK. Or i have to give g(x) and
h(x) separatel
Dear Maria,
I am not sure but something you should look further is the rotation
around your P3-O2 bond (which is P8-O7 in Tieleman's topology).
It is described by the first two lines of your dihedral section
topology:
1 2 3 6 10.0 1.05 3
1 2 3 6
Hi Gromacs users,
When I run grompp for 16 nodes to prepare my file for parallel run on my
cluster, and also -shuffle to spread the load evenly over the nodes, I
find that the position restraints get shuffled as well. This is my
command line:
grompp -v -f heat.mdp -c min_end.pdb -p dmpc_npa
Vitaly Chaban wrote:
Dear Gromacs Site Maintainers,
A few days ago I tried to upload the topology of a new system
(swcnt_dmso.zip) through this form:
http://www.gromacs.org/component/option,com_docman/task,upload/Itemid,26/
It seems all was right but I don't see my topology in the list of
avai
Dear Gromacs Site Maintainers,
A few days ago I tried to upload the topology of a new system
(swcnt_dmso.zip) through this form:
http://www.gromacs.org/component/option,com_docman/task,upload/Itemid,26/
It seems all was right but I don't see my topology in the list of
available ones till now.
I
Quoting [EMAIL PROTECTED]:
> Dear gromacs user,
> I am doing simulation of Gal1P protein in explicit solvent.when i did
> energy minimization of system i got this warning:-
> Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is
> larger than the 1-4 table size 1.000 nm
> These
Dear gromacs user,
I am doing simulation of Gal1P protein in explicit solvent.when i did
energy minimization of system i got this warning:-
Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulat
On Mon, 12 May 2008 15:10:32 +0530
"Anamika Awasthi" <[EMAIL PROTECTED]> wrote:
Dear Friends,
If my simulation crashed because of power failure, then as I know
there are two option to restart the Job.
One is GROMPP and another is 'tpbconv', in 'grompp' we have to do
some changes i
Dear Friends,
If my simulation crashed because of power failure, then as I know
there are two option to restart the Job.
One is GROMPP and another is 'tpbconv', in 'grompp' we have to do
some changes in md.mdp, but 'tpbconv' takes everything automatically,
tpbconv needs only .trr a
On Mon, 2008-05-12 at 17:25 +1000, Mark Abraham wrote:
> However unless one is comfortable removing the old lam package to avoid
> conflicts, it is much simpler (and still correct) for a user new to MPI
> compilation of GROMACS to simply install the package lam-devel using the
> mechanism for t
Jussi Lehtola wrote:
On Mon, 2008-05-12 at 13:43 +0700, Dmitri Dubov wrote:
Dear GMX users,
Sorry for my stupid question, but unfortunately I'am very poor
programmer...
Earlier I have installed gromacs 3.3.3 under SUSE Linux 10.3 both in
single and in double precision mode. Both versions work
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