Hi
what command and what option apply solvent except water in MD simulation by
gromacs.
Any help will highly appreciated!
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leila karami wrote:
Hi
what command and what option apply solvent except water in MD simulation
by gromacs.
Any help will highly appreciated!
WHat do you mean?
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University.
Dear David
in genbox command system solvated by water molecule by default. but I want
solvent except water.
leila karami
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leila karami wrote:
Dear David
in genbox command system solvated by water molecule by default. but I
want solvent except water.
leila karami
OK, now I understand.
You can give to genbox any solvent that you like, provided that each
molecule consists of a single residue (the residue
Hi
I want to use a solvent with two types molecules (for example linear and
cyclic Glucose form).
How can I fill box with them?
I highly appreciate for advice given me!
Best Regards
Rasoul
On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
leila karami wrote:
rasoul nasiri wrote:
Hi
I want to use a solvent with two types molecules (for example linear and
cyclic Glucose form).
How can I fill box with them?
You can use genbox with mixed solvents.
I highly appreciate for advice given me!
Best Regards
Rasoul
On Sat, Jan 16, 2010 at 11:42 AM,
David van der Spoel wrote:
rasoul nasiri wrote:
Hi
I want to use a solvent with two types molecules (for example linear
and cyclic Glucose form).
How can I fill box with them?
You can use genbox with mixed solvents.
There are even how-to's on the Gromacs site to accomplish this:
From what I can find, it seems that you are correct to assume that
frozen coordinates should not be scaled:
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html
and, from the online manual:
freezegrps:
Groups that are to be frozen (i.e. their X, Y, and/or Z position
chris.ne...@utoronto.ca wrote:
From what I can find, it seems that you are correct to assume that
frozen coordinates should not be scaled:
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and,
from the online manual:
freezegrps:
Groups that are to be frozen (i.e. their
Hi,
Firstly, regarding my last email, even though I didn't get any complain
about the nonsense setting for the wall_atomtype from grompp, the mdrun is
crashed after some steps.
Then I tested some atomtypes which have been given in OPLS, and checked the
output in md.log:
a) When wall_atomtype =
Hello,
I have a run that was working fine under parallel mdrun -pd and when I
then switched to domain decomposition I got:
Fatal error:
The size of the domain decomposition grid (1) does not match the
number of nodes (8). The total number of nodes is 8
while running like this:
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