Re: Spherical restraints

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 06 2021 - 11:17:11 CDT

Hi Yasser, which NAMD version and build are you running on the GPU?
Colvars doesn't make use of the GPU, but only of CPU code. So the only way
that the CPU and GPU versions may differ is if the forces applied by
Colvars are exceedingly large, and the GPU NAMD build can't deal with them
correctly.

Is the initial configuration compatible with the restraint? You can add
outputEnergy to the restraint, or (if that's the only custom force in your
workflow) look at the MISC column of the NAMD output.

Giacomo

On Tue, Apr 6, 2021 at 11:50 AM Almeida-Hern√°ndez, Yasser, Dr. <
yasser.almeida-hernandez_at_uni-due.de> wrote:

> Hi Giacomo,
>
>
> Thank you for your reply. Yes, that was the problem.
>
>
> The setting looks now like:
>
>
> set config "
>
> colvar {
> name LIG_sphere
> distance {
> group1 {atomNumbers 704} # Cu2+ cation
> group2 {atomNumbersRange 707-734} # Ligand
> }
> }
>
> harmonicWalls {
> colvars LIG_sphere
> outputEnergy on
> lowerWalls 0
> upperWalls 15
> forceConstant 1000
> }
> "
>
> colvars on
> cv config ${config}
>
>
> Now, if I run it in my laptop it works well, but if I run it in a cluster
> with GPU (namd2 +idlepoll +isomalloc_sync +p46 +devices 0,1 $INP.conf >
> $INP.log), it writes -nan values:
>
>
> TIMING: 89000 CPU: 686.545, 0.0172745/step Wall: 737.674,
> 0.0173574/step, 4.39239 hours remaining, 672.355469 MB of memory in use.
> ENERGY: 89000 nan 888064.2004 nan
> nan nan 0.0000 0.0000
> 0.0000 nan nan nan
> nan -nan nan nan
> nan nan nan nan
>
> Any thoughts?
>
> Best
>
> ------------------------------
> *From:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> *Sent:* Tuesday, April 6, 2021 5:06:58 PM
> *To:* NAMD list; Almeida-Hern√°ndez, Yasser, Dr.
> *Subject:* Re: namd-l: Spherical restraints
>
> Hello Yasser, there are a few things to check, but the first one would be
> to make sure that you actually loaded that configuration. There will be a
> (fairly verbose) set of messages printed when you do.
>
> What you did there is setting a string variable "config" to contain the
> configuration text, which can be used in a Tcl script but you actually need
> to load it afterwards, e.g.:
>
> cv config ${config}
>
>
>
> On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hern√°ndez, Yasser, Dr. <
> yasser.almeida-hernandez_at_uni-due.de> wrote:
>
>> Hello,
>>
>>
>> I want to spherically restrain a ligand around a Cu2+ cation with
>> harmonic walls. For this, I am using the colvars module as:
>>
>>
>> # Restraint the ligand in a sphere of r=15 AA around the Cu2+
>> set config "
>>
>> colvars on
>>
>> colvar {
>> name LIG_sphere
>> distance {
>> group1 {atomNumbers 704} # Cu2+ cation
>> group2 {atomNumbersRange 707-734} # Ligand
>> }
>> }
>>
>> harmonicWalls {
>> name LIG_sphere
>> colvars HL
>> outputEnergy on
>> lowerWalls 0
>> upperWalls 15
>> forceConstant 1000
>> }
>> "
>>
>>
>> ... but it doesn't work. The ligand tumbles all around.
>>
>>
>> Am I missing something? Any help will be appreciated.
>>
>>
>> Best,
>>
>> Yasser
>>
>>
>> --
>> Dr. Yasser Almeida-Hernandez
>> Postdoctoral Researcher
>> Computational Biochemistry group
>> T01 R03 D45
>> Faculty of Biology
>> University of Duisburg-Essen
>> Universitätsstr. 2, 45117 Essen
>> Email: yasser.almeida-hernandez_at_uni-due.de
>> <%20yasser.almeida-hernandez_at_uni-due.de>
>> Phone: +49 201 183 2457 <+49%20201%20183%202457>
>>
>>

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