Exactly. So now is the time for skillful scripting.
Erik
Nilesh Dhumal skrev 2011-05-20 15.31:
I used the same topology file to run 256 water molecules simulation and I
got the proper result (compared with reported one).
The problem is to visualize the trajectory in VMD since gromacs fails to
write valid pdb files when the coordinates are too large.
Nilesh
On Fri, May 20, 2011 5:22 am, Erik Marklund wrote:
Justin A. Lemkul skrev 2011-05-19 22.42:
Vitaly Chaban wrote:
For vacuum systems, "pbc = no" in conjunction with zero cutoffs is
correct to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Setting a box size and using "pbc = xyz" precludes the use of infinite
cutoffs, which should be the most rigorously correct way to treat this
type of system. With PBC, there are long-range effects that should be
avoided.
Nilesh: visualize your system, using VMD or ngmx. The behavior of
your molecular cluster during the first ps will provide an answer. Are
you sure that your topology is healthy?
I agree with this. The system should be going absolutely haywire :)
-Justin
Yes, this is a good test, and the topology should be inspected. However,
the observed result is expected for this system. A water dimer coupled to a
thermostat will dissociate eventually (pretty rapidly) at 300 K. The water
molecules themselves seem intact. The problem with visualization comes
from the fact that gromacs fails to write valid pdb files when the
coordinates are too large. I called this a bug on the developer list one
or two years ago since this generates pdb files that gromacs itself can't
read, but the other developers didn't catch on. You can postprocess the
pdb and cap the coordinates so that they're confined to the range that the
pdb format allows, but note that this will mess up the water moleucles as
they get very far apart.
Erik
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
