From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat May 19 2012 - 15:11:55 CDT
Hi Niklaus,
This is very intriguing. Can you please send me off-list the minimum
files needed to reproduce the issue?
Thanks,
Jerome
On 18 May 2012 16:13, Niklaus Johner <nij2003_at_med.cornell.edu> wrote:
> Hi all,
>
> I'm having the same issue with an FEP calculation of the protonation of a
> sidechain.
> My FEP calculations run fine as long as I don't use colvar to add a
> restraint. If I turn colvar on and add a restraint between an atom from my
> vanishing sidechain and any atom in my system but the appearing sidechain,
> it also works fine. But if I add a restraint between atoms from the
> appearing and vanishing sidechain, then it crashes at the first time step
> (even if I use forceConstant=0).
>
> It seems that adding a restraint between the vanishing and appearing atoms
> somehow makes them see each other and clash. Maybe it breaks the automatic
> generation of the non-bonded exclusion list?
>
> I tried this on namd2.7, namd2.8 and namd2.9.
> I haven't tried to use alchemify to create the exclusion list myself yet.
>
> Any input would be welcome.
>
> Best,
>
> Niklaus
>
> Niklaus Johner
> Weill Cornell Medical College
> Harel Weinstein Lab
> Department of Physiology and Biophysics
> 1300 York Avenue, Room D-501
> New York, NY 10065
>
>
>
>
>
>
>
> On Apr 24, 2012, at 8:19 AM, Jérôme Hénin wrote:
>
> Hi Jeremy,
>
> On 23 April 2012 23:38, Jeremy Parlin <jeremyparlin_at_gmail.com> wrote:
>
> I have a system with an ion bound in a protein pocket, with one distance
>
> restraint on it set via colvars. I am trying to perform an FEP simulation,
>
> where that ion changes species, while the colvar restraint stays applied.
>
>
> I've set this system up, with both ions present in the topology file, having
>
> the same initial coordinates, with the old ion set to annihilate and the new
>
> one to exnihilate. This executes successfully, however, in the early stages
>
> of the simulation, the new ion swims out of the pocket, since it experiences
>
> no protein interactions holding it there. To remedy this, I've tried to 'tie
>
> together' the two ions. I've tried to do this either with a colvar distance
>
> constraint between the two ions (restraining the distance to zero), or by
>
> creating a virtual bond in the PSF file (adding a corresponding term to the
>
> parameter file). In either case, the simulation fails on the very first
>
> step, with both ions having infinite velocity.
>
>
> This indicates that something is wrong in the way the simulation is
> set up. The two ions should not interact with each other.
>
> Thoughts on how to do this successfully? I'd really like to the exnihilated
>
> and annihilated ions to be in effectively the same position as one another
>
> at all times, but both to be allowed to fluctuate together within the
>
> binding pocket subject to my colvar restraint.
>
>
> The strategy you describe is perfectly fine and should yield the
> result you want.
>
> Now, the problem is probably with your "alchfile" - check that the
> alchemical flags are properly set to -1 and +1 on the two ions, and
> check NAMD's standard output at startup to see if everything is parsed
> as intended. If you can't find the issue, send us a compressed log
> file.
>
> Last thing: make sure you use a recent version of NAMD, ideally the
> latest, as these things are more automated in recent versions.
>
> Jerome
>
>
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