[gmx-users] mistake!!

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 13 11:54:46 CEST 2008

sarbani chattopadhyay wrote:
>   Hi everybody,
>                       My question is regarding the consequence of a 
> mistake of mine.
> I wanted to run gromacs with "charmm" force field and "tip3p" water model.
> I had posted a query as to how can I  get the "tip3p.gro" file. I was 
> suggested to equlibrate
> the "spc216.gro" file for 1ns.
> However, what I did was that I equilibrated the "spc216.gro" file but 
> while giving the
> "pdb2gmx" command , I gave the option "-water spc". I know this was 
> extremely stupid on
> my part.
> Thus now the water model selected is spc ie. it refers to "spc.itp" but 
> uses the equlibrated
> file "spc216.gro"
> Will this affect my simulation adversely? Please suggest as what can be 
> the probable
> consequences.

Force fields are designed for use with specific water models.  Using CHARMM + 
SPC is not a valid combination (see below).

> Moreover while going through some of the tutorials such as " Molecular 
> Dynamics
> Simulations" by Erik R. Lindahl, I found that "spc216.gro" can be used 
> for "tip3p"water
> model, if we correctly select "tip3p" as the water model.


> I think if I choose "tip3p" as the water model and the equlibrated 
> "spc216.gro" file , then I
> should get thecorrect results.Is this so?

Almost.  There is something unique about the CHARMM water molecule - there are 
L-J parameters for the hydrogens.  Therefore, the water model you need is 
tip3p-charmm.itp (packaged with the CHARMM for GROMACS download that you 
probably got from the downloads site).  So you will need to manually edit your 
.top file, regardless of what pdb2gmx gives you, to include this proper water model.


> Thanks in advance.
> Sarbani
> Rediff Shopping 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> ------------------------------------------------------------------------
> _______________________________________________
> 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


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list