From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Dec 05 2014 - 14:49:55 CST
alchLambda2 is optional as of the 2014-12-05 nightly build. -Jim
On Thu, 4 Dec 2014, hannes.loeffler_at_stfc.ac.uk wrote:
> Hi Jim,
> many thanks. One other point to consider may be that the code checks if alchLambda2 is set. I think for TI calculations this is not needed.
> I have made some tests in the meantime computing relative hydration free energies and I believe that this _may_ work. The reason why I am not fully sure yet is how the particular alchemical implementation works in NAMD. With NAMD I can only define disappearing or reappearing atoms but not direct scaling of one atom type into another (would require scaling of all bonded terms). I can "mimic" this with a phase-in-phase-out scheme, i.e. annihilate one atom type and recreate it as that of the final state. But the practical problem is the charge as I may end up with a non-zero net charge in one of the partitions. A way around this is to go "full" dual topology i.e. annihilate the first state and exnihilate the other... I guess this all works nicely with the example in the manual and the CHARMM force field which defines IIRC charge neutral groups (or integral charged if necessary). I am dealing, however, with "arbitrarily" parameterised organic ligands.
> Many thanks again,
> From: Jim Phillips [jim_at_ks.uiuc.edu]
> Sent: 04 December 2014 17:09
> To: namd-l_at_ks.uiuc.edu; Loeffler, Hannes (STFC,DL,SC)
> Subject: RE: namd-l: Re: alchemical free energy simulations with parmtop
> Hi again,
>> From checking my old emails it appears I added the test to disallow
> alchemical simulations with AMBER parameters because one of our free
> energy gurus unfamiliar with the details of the code thought there was
> likely an issue. On further inspection AMBER parameters should work fine,
> so I've removed that check but added some warnings for VDW switching
> options (off, force, or Martini) that will not be used for alchemical
> interactions (but will apply to interactions not involving product or
> reactant atoms). These changes are in the 2014-12-04 nightly build.
> Thanks for pointing this out.
> On Tue, 2 Dec 2014, hannes.loeffler_at_stfc.ac.uk wrote:
>> 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 [jim_at_ks.uiuc.edu]
>> Sent: 02 December 2014 18:06
>> To: namd-l_at_ks.uiuc.edu; 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.
>>> On Tue, 17 Jun 2014 10:35:59 +0100
>>> Hannes Loeffler <Hannes.Loeffler_at_stfc.ac.uk> wrote:
>>>> 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,
>>> Scanned by iCritical.
>> Scanned by iCritical.
> Scanned by iCritical.
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