[gmx-users] parameters obtained after NPT

[soumadwip ghosh]

Thanks Justin for a prompt reply.
 Currently I am working with 4.5.6 and CHARMM 27 as I mentioned and I was
wondering whether correct parameters can be obtained after NPT without
really upgrading the software version because some of my previous results
are obtained by working with 4.5.6 and CHARMM27 where I dint encounter such
errors. When I view the trajectory using VMD the box looks deformed and the
water molecules are not well distributed. It might sound unrealistic but is
there a possibility by which I can fix these errors in 4.5.6 and get the
parameters right?

Is it a problem that I am doing NPT first and then going for NVT. Ideally,
it should'nt be a problem right?

If my system is still blowing up why those nasty errors are not occurring
this time? Do u suggest me to minimize the energy further? The potential
got converged in the first attempt and thats why I was to equilibrate my
system.

How can I ensure that by upgrading the version and using correct mdp
parameters I wont be facing such errors? I mean are systems such as mine
(CNT+DNA) known to have problems in equilibration in CHARMM27 (NPT with
position restraints)?

Your advise as always would be a big help. Thanks

Soumadwip Ghosh
Research Fellow, IITB
India.