From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Oct 08 2012 - 07:10:57 CDT
Please also note the following lines:
00269 if (((finalRMS <= initialRMS && targetRMS <= curRMS) ||
00270 (finalRMS >= initialRMS && targetRMS >= curRMS) ||
which mean that the bias applied is not a traditional harmonic
potential, but rather a half-harmonic potential that only acts one
way. That is not very clear in the documentation.
On 5 October 2012 22:47, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> I think you're right. That being said, the choice of k in TMD is rather ad
> hoc anyway, so it doesn't matter terribly much. Obviously it can't be fixed
> in the code (or would mess up all previous configs), but a change to the
> manual should be mostly harmless. One would just have to change the
> equation to be k, not k/N, but note that k is effectively scaled by N in the
> force (so really nothing changes in how one thinks about it). It makes
> sense intuitively anyway that k should NOT be scaled in U, which is the
> potential for the ENTIRE domain, but will be scaled (once) in F, which is
> applied to INDIVIDUAL atoms.
> I'm copying the last person to work on that part of the code to see if he
> On Oct 5, 2012, at 3:01 PM, Mert Gür wrote:
> Hi JC,
> Thanks a lot for your response.
> The potential in TMD is
> U= 0.5 k/N ( RMS(t)-RMS*(t) )^2
> If you take the gradient of it then the force becomes (According to my
> F= -k/N^2 ( 1-RMS*(t)/RMS(t) ) (R-R_target)
> So there is an extra N. Does " k = K/it->second.size()" takes care of that ?
> I use the following definition for RMS. Maybe the person who implemented it
> used a different definition.
> I am sending you a separate e-mail with my detailed derivation.
> On Fri, Oct 5, 2012 at 2:26 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>> What about this line?
>> k = K/it->second.size();
>> On Oct 2, 2012, at 12:43 PM, Mert Gür wrote:
>> Dear all,
>> I wonder if the equation shown in the following link is correct?
>> Is it k or k/N. If it is k/N (as written in the link) then there must be a
>> second division by N in the source code
>> which I can not find.
>> Can anyone comment on this?
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