uot;David Mobley" <[EMAIL PROTECTED]>
> > > Reply-To: Discussion list for GROMACS users
> > > To: "bharat v. adkar" <[EMAIL PROTECTED]>
> > > CC: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] soft-core and c
ussion list for GROMACS users"
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 16:17:36 -0800
Berk,
> But what do you mean with charging and discharging?
>
> Going one way or the other in lambda does not matter.
> What matters is if there a
OTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 16:17:36 -0800
Berk,
> But what do you mean with charging and discharging?
>
> Going one way or the
verse.
David
> Berk.
>
>
> >From: "David Mobley" <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users
> >To: "bharat v. adkar" <[EMAIL PROTECTED]>
> >CC: Discussion list for GROMACS users
> >Subject: Re: [gmx-users] s
t; <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "bharat v. adkar" <[EMAIL PROTECTED]>
CC: Discussion list for GROMACS users
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 10:26:37 -0800
Following up on this is
Following up on this issue, discharging phenol in water appears to
give the same results as charging phenol in water. In other words, so
far the only cases for which there seem to be a problem are relative
calculations (and so far I haven't looked at this for any other than
Bharat's test cases).
B
problem) could
give small errors that one might not notice directly...
Berk.
From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "bharat v. adkar" <[EMAIL PROTECTED]>
CC: Discussion list for GROMACS users
Subject: Re: [
Hi, Bharat, and David vdS.
This indeed is looking suspiciously like a real problem. FWIW, I did
reproduce your original problem using my own input files and PME with
gromacs 3.3.1.
It's still a bit perplexing, in that you seem to be getting basically
the "right" answers for the forward transforma
bharat v. adkar wrote:
Hi David,
I am keeping the subject same so that it is helpful to track in
future :)
On Sat, 10 Nov 2007, David Mobley wrote:
Dear Bharat,
OK, I went ahead and ran with your topologies using my own run
scripts. My runs haven't finished yet, but looking at just
Hi David,
I am keeping the subject same so that it is helpful to track in
future :)
On Sat, 10 Nov 2007, David Mobley wrote:
Dear Bharat,
OK, I went ahead and ran with your topologies using my own run
scripts. My runs haven't finished yet, but looking at just
values from equilibrati
Bharat,
Your values for the first set of calculations (the forward case?)
below look really weird. I suspect you have something messed up in
those runs. Have you checked that your define statements worked
properly, and checked your run input files? In particular, your
is staying almost constant a
hi,
i am pasting the xmgrace file for the both forward and reverse
transformation of charge modification for Ala->Gly mutation.
The simulations are performed in water. when you open the file with
xmgrace, you can clearly see the behaviour what i was describing in
previous mails.
bharat
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse
transformation onto that of forward with both axes reversed. so i
should expect overlap. this is consistent with whatever you are saying. i
am sorry for negligence and confusion.
Hi,
> i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse
> transformation onto that of forward with both axes reversed. so i
> should expect overlap. this is consistent with whatever you are saying. i
> am sorry for negligence and confusion.
And taking the negative?
> >> but wh
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
it is fairly straight FORWARD.. forward is from state A to state B, and
reverse is from state B to state A. Say for example, forward
transformation is going from ethane to methane. in this step, i define
three of the terminal hydrogen on say C2, with
Hi,
> it is fairly straight FORWARD.. forward is from state A to state B, and
> reverse is from state B to state A. Say for example, forward
> transformation is going from ethane to methane. in this step, i define
> three of the terminal hydrogen on say C2, with zero charges and C2 with
> charge o
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
Everything goes fine till this point. Now, i do reverse transformations to
check for hysteresis. For vdw transformations, i get almost perfect
overlap of dG/dlambda vs lambda for forward and reverse transformations,
but for coloumb transformations, i
Hi,
> Everything goes fine till this point. Now, i do reverse transformations to
> check for hysteresis. For vdw transformations, i get almost perfect
> overlap of dG/dlambda vs lambda for forward and reverse transformations,
> but for coloumb transformations, if i don't use soft-core potentials,
Dear all,
i am trying some very basic transformations by thermodynamic integration
to calculate free energy difference. By following mailing-list archive, i
learned that it is efficient to do coulomb transformations and LJ
transformations separately. i use David Mobley's tutorial values for
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