Unless you specifically set the PME parameters in mdin they are inferred
from the box dimensions in inpcrd. If you are running NVT, I can't imagine
this ever causing a problem. However, when running NpT, it is possible that
the PME grid parameters or coefficient change at the restart because a
different box size is encountered (it would probably have to be a big
change though...).
Most uses of imin = 5 are for GB, which bypasses the PME code path entirely
and this is therefore irrelevant.
As I stated in a previous post. There is not, to my knowledge, *any*
functional difference between the two protocols that you described, other
than the fact that the PME grid can be set up differently for each
structure (but do you really want to do that?).
Regards,
Brian
On Fri, Aug 1, 2014 at 4:18 AM, ye renlo <renloye.gmail.com> wrote:
> Dear AMBER users,
> When I finished a MD simulation, I want to perform energy minimization on
> some structures in MD trajectory, now I have two methods to do that.
>
> 1. extract desired frames from trajectory and save the frames as *rst*
> files, set *imin=1* in control file
>
> 2. extract desired frames from trajectory and save the frames as *crd*
> files, set *imin=5* in control file, use -c and -y flags for sander
>
> Other parameters are same for both methods
>
> for imin=5, the following important note is presented in amber manual:
> **IMPORTANT CAVEAT: The input coordinate file used (-c <inpcrd>)
> should be the same as the input coordinate file used to generate the
> original trajectory.
> **This is because *sander sets up parameters for PME from the box
> coordinates in the input coordinate file*.
>
> My questions are:
> 1. What does it mean "*sander sets up parameters for PME from the box
> coordinates in the input coordinate file*"? What if I chose a different
> <inpcrd> for -c flag(i.g., md rst file)
> rather than the original <inpcrd> file generated by Leap?
>
> 2. I have tried two methods mentioned above and finds that the first
> method with "*rst file,imin=1*" gives a lower final enery than the second
> method with "*crd file, imin=5*".
> Could someone tell me what's the difference between imin=1 and imin=5
> when performing minimizations on structures from MD trajectory
>
> Many thanks!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Fri Aug 01 2014 - 06:30:02 PDT
