Am 17.03.2014 20:11, schrieb
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:
Dear gromacs users
>
>I will use pull = constraint (constraint pulling) for PMF calculations.
>
>There is a tutorial about PMF from Justin in which he used
>pull = umbrella (umbrella sampling).
>
>In justin tutorial,
Hi,
I'm no expert for this stuff, but could it be that you generate about 40
of the #my_mol.log.$n# files (probably only 39)?
It could be that the 'mpirun' starts 40 'mdrun'-jobs and each generates
its own out put.
For GROMACS 4.6.x I always used
mdrun -nt X ...
to start a parallel run (where X
roblem. On Fri, Jan 24, 2014 at 6:18 PM, Thomas
Schlesier wrote:
>Hi all,
>I am having problems with GROMACS 4.6.5 and one type of CPU on our cluster
>(other CPU-types make no problems). GROMACS was always compiled on the
>master, which uses a different CPU-type (see below at the beg
Hi all,
I am having problems with GROMACS 4.6.5 and one type of CPU on our
cluster (other CPU-types make no problems). GROMACS was always compiled
on the master, which uses a different CPU-type (see below at the
beginning of the 'md.log'-file).
For the CPU type (partial output from 'cat /proc
Since the spring has a finite force constant, it is quite naturally that
one observes fluctuations in the distance (between reference and pulled
group) and forces.
Greetings
Thomas
Am 11.01.2014 22:45, schrieb
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:
Hi,
>
>Dear Gromacs Users
>
>I
Dear all,
I have found that the GAFF force field is used in concert with the AMBER
fore fields. Since both force fields use the same [ defaults ] section
in the forcefield.itp files, I think GROMACS can come up with nonbonded
parameters between these force field.
But since both force fields us
uring pulling, but I am not
able to achieve this. It is quite mysterious.
Vitaly
Dr. Vitaly V. Chaban
On Mon, Dec 2, 2013 at 10:18 AM, Thomas Schlesier wrote:
>Hi,
>I never used the pull-code with GMX 4.5.x or 4.6.x,but I would assume that
>it'sthe same as in 4.0.x:
>'Um
Hi,
if you create the topol.top with 'pdb2gmx', the values for all the
parameters are not listed in the topology. Only all the atom numbers,
from these GROMACS can search the atom- and/or bondtypes and then it
constructs the bonded parameters. If any parameters are missing 'grompp'
will compla
Hi all,
for the COOH terminal group one of the angles (the one including two
carbons and the oxygen which carries the hydrogen) does not get
overwritten by aminoacids.c.tdb.
Ok, somewhat slower:
Used ASPH as a test molecule and chose a -COOH capping group.
From aminoacids.rtp:
[ ASPH ]
[ at
Hi,
for GMX 4.0.7 and GMX 4.6.5 is a typo in the aminoacids.rtp file (but i
would assume that it affects the whole 4.X.Y series).
[ ASPH ]
[ atoms ]
...
OD1opls_269 -0.530 3
OD2opls_268 -0.440 4
HD2opls_2700.450 4
...
The charges of OD1 and OD2 should
Hi,
I never used the pull-code with GMX 4.5.x or 4.6.x,but I would assume
that it'sthe same as in 4.0.x:
'Umbrella': Due to the harmonic potential the force and the distance
between the two particles will fluctuate.
'Constraint': Only the force will fluctuate. The (relative) distance
between th
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