RE: Re: alchemical free energy simulations with parmtop

Date: Tue Dec 02 2014 - 12:39:41 CST

Hi Jim,

many thanks for your reply.

I am not sure though if I fully understand what you are saying besides that I should give it a try. I see that this was changed in rev 1.1439 of src/SimParameters.C (by 'jim', is that you?) and naturally I was wondering if there is a deeper reason for that.

The most obvious question to me is if I have to modify the parmtop file to get this working. I have found the code which deletes all bonded terms between the appearing and disappearing atoms. I have not yet found the bit which does this for the non-bonded parameters although I should be able to do just that by adding appropriate exclusions in the parmtop file.

Can namd do alchemical simulations in vacuo?


From: Jim Phillips []
Sent: 02 December 2014 18:06
To:; Loeffler, Hannes (STFC,DL,SC)
Subject: Re: namd-l: Re: alchemical free energy simulations with parmtop

There is nothing obvious to me. I can understand certain switching
options not being supported, so perhaps AMBER has a different default.

You can certainly remove the check and try.


On Mon, 1 Dec 2014, Hannes Loeffler wrote:

> Right. So namd explicitly disallows alchemical simulations when amber
> is on. The error message is a bit weird though as it says that "AMBER
> parameters" are not supported. A particular parameter set in itself can
> hardly be the reason as it should be possible to introduce those trough
> the PSF or Gromacs .top route (although the particular functional form
> of the AMBER force fields may not be fully supported). I can't see
> any safeguards against this in the code.
> So, the question: why would the AMBER _force field_ not be supported?
> Apparently there are a few differences in the functional forms of the
> CHARMM and AMBER force fields which lack support for instance.
> Cheers,
> Hannes.
> On Tue, 17 Jun 2014 10:35:59 +0100
> Hannes Loeffler <> wrote:
>> Hi,
>> I am just looking through a few tutorials on how to do alchemical
>> relative free energy calculations and see that they are all based on
>> the PSF topology file format. I wonder if this is a requirement with
>> namd or a AMBER parmtop file could be used instead.
>> From what I understand there could be problems with the force fields
>> terms in the parmtop because the way it works in namd is to create the
>> morph pair as a single residue (and describe vanishing/appearing atoms
>> in an associated PDB file). But is it possible with a parmtop
>> provided the parmtop is created/manipulated accordingly? I guess
>> this all boils down to how namd generates the force field terms
>> internally for the two mutated molecules/fragments.
>> Many thanks,
>> Hannes.
> --
> Scanned by iCritical.

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