20 maj 2007 kl. 20.59 skrev David van der Spoel:
Dmitriy Golubovsky wrote:
Dear Guru!
have you got any idea, on what how to calculate pH. for the system?
i'm solving a promblem of coil-globule transition for polymer.
do the topology for my structure(opls ff), do MD in water (spc).
get the statiscts. everything is ok.
the summary charge is equal to zero. no dissociation.
so the question is - how to calculate pH. or it's not possible?
if it is possible, than how to variate this pH in some range.
I allready try to use genion, but didn't get good results, on case
of very big dependence of the results from the initial
conformations of ions.
How about computing the H3O+ concentration?
It is close to impossible to simulate realistic pH with limited
size systems. In practice your pH is always seven.
Depending on your specific application, CPHMD can be used to simulate
with constant pH. Unfortunately, CPHMD utilizes lambda-dynamics,
which is not yet implemented in gromacs. It should not be THAT hard
to implement yourself if you know a thing or two about MD and
programing in general.
/Erik
What do you mean with "no dissociation"?
--
David.
______________________________________________________________________
__
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
