sapna sarupria wrote:
Dear users,
I had posted this question earlier too but did not get any response.
I am re-posting it hoping someone can clarify this for me.
I performed NPT simulations of few different systems using both
gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting
files, topology files etc for both the versions. The systems are pure
water system (spc/e 10684 water molecules) and a protein-water system.
However, the average volume of the system that I get is from the
simulations is different for the two versions. In case of pure water,
gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1
(~324.604 nm^3) and the difference is significantly higher than the
fluctuations in the volume. The pressure is maintained at 1 bar and the
temperature is maintained at 300 K using Berendsen barostat and
thermostat respectively. I used SETTLE to maintain water geometry. I was
wondering if someone could tell me why this happens? Has there been a
modification in the pressure virial calculation or something related to
the same that leads to these differences?
Have you checked the energy differences?
Have you compared tpr files?
Is the dispersion correction on and are you using some kind of
shift/switch? (This has changed between 3.2 and 3.3).
If you can not find the reason for this and it is reproducible then
please submit a bugzilla with a 3.2.1 tpr file that reproduces the problem.
Thank you
Regards
Sapna
--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
