[gmx-users] 3-site methanol model (Re: C. Freudenberger)

Nuno R. L. Ferreira nunolf at ci.uc.pt
Wed May 21 16:15:01 CEST 2003

Hi Christoph Freudenberger

Yes, you may say I'm lucky. Choose one, you may say that. Actually, I've saw
your box in the molecules directory in GROMACS contributions, in April. When
I was talking about the 3-site model, I was refering to your methanol box

Already runned a 1 ns MD with your equilibrated methanol box, and the Dt is
OK, 1.6 10-5 cm2 s-1, just like the one presented by WFG in his 2000 JCP
The 6-site methanol model that I talked about in the last e-mail posted in
this gmxuser's list , is from charmm forcefield. But this molecule is
categorized in the forcefield as a model molecule, so its still on a
experimental basis, I presume. As you might know ,the academic version of
CHARMM has no support, so I'm alone to talk about their model. Have to do a
net search about using methanol within CHARMM.

My questions are :

1 ) I want to do a MD simulation of a peptide in methanol. Right know, I'm
interested in the diffusion coefficient of the protein and also on the Dt of
the solvent, not just the bulk one, but to see if I can descriminate a kind
of hydration shells around the solute. If your model is good enought to
mimic the bulk methanol experimental Dt, think might give me other good Dt's
, concerning the solvent, in comparison to the 6-site model, that, as I said
last e-mail, was about 1.8 10-5 cm2 s-1. Is this "true" ?

2) When performing methanol Dt calculations around the peptide, what is the
best way to do this ? I mean, should I fixe the peptide all along the MD, or
let it translate?

3) Took a look at your methanol .itp. Don't understand how you translated
the Lenard-Jones parameters from WFG JCP 2000 article to your topology file.
It's just a curiosity. If I have some more doubts about your meoh box
implementation, I'll contact you on this list

Best regards,
Obrigado (thank you)

P.S.Have to say I'm not a physicist or even a chemical physics guy. This
moment I'm a 75% BIOchemist. The rest is turning to MD's and NMR, and still

Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra

Phone: +351 239 852080
Fax: +351 239 827703

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