Please do not include the text of the digest when composing a message. It
throws off searches of the archives.
rituraj purohit wrote:
Dear Friends,
During first step of MD (pdb2gmx) I come to know that my protein having
net charge -42 e (it has two chain, A and B each having -21 e ).
Why neutral system is preferable for further steps of MD & what kind of
problem encounter with charged system ?
There are theoretical reasons for not simulating a system with a net charge, but
more intuitively, life does not exist at net charge. For every positive, there
is a negative somewhere.
Should i have to add 21 Na+ to make it neutral, through "genion"?
No, you should add 42 Na+, since your system has a net -42e charge.
-Justin
Regards,
Rituraj
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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/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/mailing_lists/users.php
