From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jun 28 2017 - 11:35:19 CDT
Hi Francesco, wrapAll is not recommended for a system where more than one
molecule is involved in the variables' definition:
http://colvars.github.io/colvars-refman-namd/colvars-refman-
namd.html#x1-160004.3
Again, the computation of a center of mass for a group requires unwrapped
coordinates. I would double check that the same exact configuration is
being loaded into VMD, against a NAMD simulation with 0 steps.
Giacomo
On Tue, Jun 27, 2017 at 3:46 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hi Giacomo:
> I am using for ABF the last frame (.xsc file) of MD equilibration
> generated without PBCs enabled in NAMD config file. That config file only
> had:
>
> wrapNearest no
> wrapAll on
>
> If I measure directly the distance between the centers of mass of protein
> and ligand for that frame:
>
>
>> >Main< (francesco) 33 % set selprot [atomselect top "protein"]
>> atomselect3
>> >Main< (francesco) 34 % measure center $selprot
>> 326.3038024902344 453.4432678222656 342.5987243652344
>> >Main< (francesco) 35 % set sellig [atomselect top "segname SAA1"]
>> atomselect4
>> >Main< (francesco) 36 % measure center $sellig
>> 329.97216796875 441.479736328125 317.9831237792969
>>
> >Main< (francesco) 37% set dist [veclength [vecsub [measure center
> $selprot] [measure center $sellig]]]
> 27.613597797130065
> >Main< (francesco) %
>
>
> I get a result (27.6) different from "cv printframe" by loading that NAMD
> frame to VMD (18.9).
>
> Should any of these conditions be unsuitable for ABF, then, without a
> complete reeducation, it will be difficult for me carrying out an ABF for
> protein-ligand. However, I am strongly interested in that particular
> protein-ligand system, I spend a lot of time in parameterizing the ligand.
> I imagine that with FEP (not yet attempted) I'll be faced by samilar
> problems.
>
> francesco
>
>
>
> On Mon, Jun 26, 2017 at 6:32 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Francesco, when distances between groups of atoms are involved, it is
>> really important to check that the PBCs are the same in both VMD and NAMD.
>>
>> Giacomo
>>
>> On Mon, Jun 26, 2017 at 12:24 PM, Francesco Pietra <chiendarret_at_gmail.com
>> > wrote:
>>
>>> I also run the same ABF (rmsd all atoms of the ligand less methyl
>>> hydrogens) with colvar "r" = 18.9 from cv printframe (unlike the directly
>>> measured 27.6 with previous ABFs). In all cases, I took the colvars values
>>> from the last frame of the 58.2ns MD, not averages along the whole
>>> simulation)
>>>
>>>
>>> Main< (Conformation:5xxf-SAA1) 28 % cv printframe
>>>> 0 1.88926419197828e+01 5.22845307973583e+01
>>>> -3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
>>>> -5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00
>>>>
>>>> >Main< (Conformation:5xxf-SAA1) 29 %
>>>>
>>>> >Main< (Conformation:Bound_5xxf-SAA1-allH_except_methyl_H) 33 % cv
>>>> printframelabels
>>>> # step r Theta
>>>> Phi Psi theta
>>>> phi RMSD r_RMSD
>>>>
>>>
>>> The immediate (step 0) error was again atoms moving too fast, this time
>>> one heavy atom and one H-atom of the ligand.
>>>
>>> f
>>>
>>> ---------- Forwarded message ----------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Mon, Jun 26, 2017 at 12:28 PM
>>> Subject: Fwd: Atoms too fast/periodic cell too small with ABF
>>> protein-ligand
>>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>>
>>>
>>> I must add that the attempted ABF was "Conformation:Bound". For rmsd for
>>> the ligand I had chosen all heavy atoms.
>>> By choosing all atoms of the ligand, except hydrogens at the methyl
>>> groups, the simulation also crashed at the first step, this time for two H
>>> atoms of the protein, one (HG1) very far from the ligand, the other one
>>> (HA) close to the ligand.
>>>
>>> With "Conformation:Unbound" the ABF went to completion without errors.
>>>
>>> Hope this helps suggesting what to do.
>>>
>>> As I said, there was no problem with MD equilibration for this system,
>>> at the same ts=1.0fs, along a trajectory of during 58.2ns.
>>>
>>> francesco
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Sun, Jun 25, 2017 at 12:56 PM
>>> Subject: Atoms too fast/periodic cell too small with ABF protein-ligand
>>> To: NAMD <namd-l_at_ks.uiuc.edu>
>>>
>>>
>>> Hello:
>>>
>>> I am attempting a protein-ligand ABF, following the 2017 tutorial, by
>>> using a 58.2ns problemless equilibrated system (ts=1.0 fs, bond restriction
>>> on water only) in a TIP3P water box on a main pure-CPU cluster. Rather
>>> large protein, organic ligand as accurately parameterized as I could, by
>>> fitting torsions and water interaction.
>>>
>>> I am experiencing immediate "atoms moving too fast" (two H atoms of the
>>> ligand) when using a linux 4-core cpu desktop, or "periodic cell has become
>>> too small" on a linux GPU workstation. At the moment I have no access to
>>> the cluster.
>>>
>>> I used ts=1.0 fs, i.e. no bond restriction, except for TIP3P water, as
>>> in the equilibration.
>>>
>>> As a possible cause, that I was unable to verify, is the setting of
>>> Euler and polar angle in the colvars definition. That is , I used the
>>> following values from "cv printframe"
>>>
>>> >Main< (Conformation:5syf-SAA1) 28 % cv printframe
>>>> 0 1.88926419197828e+01 5.22845307973583e+01
>>>> -3.39612142392650e+01 9.26730407864645e+00 1.01135055762437e+02
>>>> -5.05311208874754e+01 0.00000000000000e+00 0.00000000000000e+00
>>>>
>>>
>>> by discarding the first two, and using the directly measured intercenter
>>> distance of 27.6A in place of 18.89 from printframe, i.e., as follows:
>>>
>>>
>>> harmonic {
>>> colvars r
>>> forceConstant 0.0
>>> centers 27.6 # OK measured
>>> }
>>>
>>>
>>> harmonic {
>>> colvars Theta
>>> forceConstant 0.0
>>> centers 52.3 # from printframe
>>> }
>>>
>>>
>>> harmonic {
>>> colvars Phi
>>> forceConstant 0.0
>>> centers -40.0 # from printframe
>>> }
>>>
>>>
>>> harmonic {
>>> colvars Psi
>>> forceConstant 0.0
>>> centers 9.27 # from printframe
>>> }
>>>
>>>
>>> harmonic {
>>> colvars theta
>>> forceConstant 0.0
>>> centers 101.1 # from printframe
>>> }
>>>
>>>
>>> harmonic {
>>> colvars phi
>>> forceConstant 0.0
>>> centers -50.5 # from printframe
>>> }
>>>
>>> Should this assignment of colvars be correct, where to look for the
>>> causes of the instability of the system?
>>> I must confess that I am the first time at such an ABF beyond the
>>> tutorial
>>>
>>> Thanks for advice
>>>
>>> francesco pietra
>>>
>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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