From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jul 05 2017 - 11:30:59 CDT
Hi Francesco, adding "wrapAll no" after running with "wrapAll yes" will not
unwrap the coordinates that were wrapped in the previous simulations. But
that's mostly a concern for a continuous over time definition of your
centers of mass.
As for the consistency, can you produce a minimal input that reproduces the
problem and include it as a download link?
Giacomo
On Wed, Jul 5, 2017 at 12:03 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hi Giacomo:
> I have now continued the "wrapall on" 58.2ns MD for further 0.11ns under
> "wrapall no". The system remains in order, except a few TIP3Ps out of the
> box margins.
> All values from "cv printframe", are substantially unchanged, except Psi,
> which has changed sign, from +166.2 to -168.1. Also the directly measured
> "r" is substantially unchanged.
>
> "r" changed from 5.97/27.6 to 5.92/27.9, where the larger value is from
> direct measurements as follows:
>
> set selprot [atomselect top "protein"]
> measure center $selprot
> set sellig [atomselect top "segname SAA1"]
> measure center $sellig
> set dist [ veclength [vecsub [measure center $selprot] [measure center
> $sellig]]]
> 27.91017455323315
>
> I loaded to VMD the DCSs from NAMD, I suppose that PBCs are the same.
> Therefore, I do not understand why "r" is so much different with the two
> methods.
>
> If - as it is likely - there is a bug in what I did, and such a bug can be
> felt, I would like to learn how to get out of this labyrinth.
>
> thanks a lot
>
> francesco
>
>
> On Wed, Jun 28, 2017 at 6:35 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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
>>
>
>
-- 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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