> Maik, what is the power you are using for soft core ?
As Berk and others suggested, sc-power = 1.
regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Thanks Berk, everything is fine at last.
I guess this is my last question : if for example I change three bond lengths
from b0A=0.1 to b0B=0.15, when I use gmxcheck with -ab, it prints only one
difference between state A and B, instead of 3. Is this ok ?
Maik, what is the power you are using
> Date: Mon, 4 Feb 2008 16:18:53 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: FEP : separating components of dgdl
>
>
>
> Thanks Maik for your parameters for amber99 soft core !
>
> Berk, you were right. The missing term is
I think, there are some "best" parameters :)
Ich tested them with some smaller systems and found, that sigma=0.3 and
alpha=0.25 seem to perform quite well.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassb
Hi,
You were right for the bonds, I forgot that I was using constraints = all-bonds.
Could the missing term be the soft core then ? Or is it included in VdW ?
Anyway, I noticed that this problem of hidden extra term happens when I modify
something else than a hydrogen. Does it make sense ?
For
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Message: 2
Date: Tue, 29 Jan 2008 10:24:57 +0100
From: "BON Michael" <[EMAIL PROTECTED]>
Subject: [gmx-users] RE : FEP : separating components of dgdl
To:
Message-ID:
Thanks for the quick reply.
I have an other question : I ran a quick simulation on a single node using
mdrun -sepdvdl and the components are written in
the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum
of the components above. Example for some step:
VdW and Coulom
> Date: Mon, 28 Jan 2008 16:44:35 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: FEP : separating components of dgdl
>
>
> Hi,
>
> I would like to know if there is a way to see the values of each components
> (angles, dihedrals
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