Re: forces on fixed atoms

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Feb 17 2011 - 03:31:32 CST

Hi Brian,

I see. What I suspect is happening is, forces between free and fixed
atoms are computed, but under normal conditions they are just not
reported for fixed atoms.

If you don't want to enable fixedAtomsForces, you could try modifying
ComputeGlobal::saveTotalForces at the end of file ComputeGlobal.C:
remove the line that says
if ( fixedAtomsOn && atoms[i].atomFixed ) f_sum = 0.;
No guarantee there, but it's worth trying.

By the way, that function is strangely written. I'd just have an
if-else there, rather than summing terms and then deciding whether to
scrap the sum and put 0 instead.

Cheers,
Jerome

On 17 February 2011 01:04, Bennion, Brian <Bennion1_at_llnl.gov> wrote:
> Hello Jerome
>
> From the manual this keyword will give you the forces between the fixed atoms as well as any forces from the free atoms correct?
> I am interested only in the forces between free atoms on the fixed atoms.
>
> Brian
>
>
> ________________________________________
> From: heninj_at_gmail.com [heninj_at_gmail.com] On Behalf Of Jérôme Hénin [jhenin_at_ifr88.cnrs-mrs.fr]
> Sent: Wednesday, February 16, 2011 3:58 PM
> To: Bennion, Brian
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: forces on fixed atoms
>
> Hi Brian,
> Try the fixedAtomsForces keyword.
> Jerome
>
> On 16 February 2011 23:01, Bennion, Brian <Bennion1_at_llnl.gov> wrote:
>> Hello,
>>
>> I have a system where I would like to know the forces acting on a set of fixed atoms by the free atoms in the system.  Initially I thought that a simple tclforces script would give me that information, however when loadtotalforces is used it appears to be zero'ed out already.
>>
>> Any thoughts?
>>
>> Thanks
>> Brian Bennion
>>
>>
>> Biosciences and Biotechnology Division
>> Lawrence Livermore National Laboratory
>> 7000 East Ave Livermore California 94550
>> phone:925-422-5722
>> fax:925-424-4334
>>
>>
>>
>>
>

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