[gmx-users] protein constrained, ligand ot constrained

Lars.Schaefer at mpi-bpc.mpg.de Lars.Schaefer at mpi-bpc.mpg.de
Sun Apr 15 18:59:46 CEST 2007

hi Luca,
I dont quite understand your point. The benefit of constraints is that
they allow you to use a larger timestep of, say, 2 fs instead of 1 fs or
so. But if you dont constrain your ligand, you have to use a small
timestep anyway, so there is no reason to constrain the protein then.
BTW: according to my experience, the main contribution to the binding
energy is electrostatics, so make sure your pointcharges are OK. No need
to worry  about the bond force constants. You want to constrain them
anyway ;-)

> Dear all,
> I would like to set up a simulation of a protein-ligand system with the
> protein left bond-constrained using LINCS algorithm and the ligand left
> unconstrained, i.e. in order to check the effect of some variations of
> force constants that I have computed on the protein-ligand interactions.
> Do you have any suggestion about this issue ?
> Actually, the only solution that I have (as suggested by someone else,
> also) is to use the mdp option
> constraints    =   none
> and write a new section for the protein topology of this kind (values
> are w/o meaning):
> [constraints]
> 1 2 1 0.150
> 1 3 1 0.179
> 2 9 1 0.130
> etc etc ... an almost simple script could do the job.
> This method seems to me, by now, the right one, but do you know any
> other more straightforward method for performing this operation ?
> Thanx in advance
> Luca
> ********************************************************************
> Sostieni la ricerca del San Raffaele con il 5permille!
> Basta indicare nell'apposito riquadro della dichiarazione dei
> redditi ("Ricerca sanitaria")
> il codice fiscale della
> Fondazione Centro S. Raffaele del Monte Tabor:
> 03 06 42 80 153 e ricordarsi di firmare.
> Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
> www.5xmille.org
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list