Re: modifying cut off

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Thu Apr 07 2005 - 19:38:03 CDT

Correct me if i am wrong, but when you use PME there is no
truncation of the electrostatics, just imposed periodicity.
However, NAMD does not always use PME every time step
(see section 5.2).

it seems to me that your stability problems are arising
from truncation changes to the vdw terms. try to set the
fullElectFrequency so that it computes everytime step,
in which case the electrostatics is truly long range.
see if your problem persists, and then it will not be
directly do the the -2 charge on the phosphate, but
probably due to the other terms. this simulation
may take a lot longer, so if time is a problem you
may want to think more first.

as far as a systematic review of cutoff, i can't give you
a reference.

someone else correct me if i am misleading michel here.

-michael

On Apr 7, 2005, at 5:01 PM, Michel Espinoza-Fonseca wrote:

> Yes
>
>
>
>
> From: Michael Grabe [mailto:mgrabe_at_itsa.ucsf.edu]
> Sent: Thursday, April 07, 2005 7:01 PM
> To: namd-l_at_ks.uiuc.edu; Michel Espinoza-Fonseca
> Subject: Re: namd-l: modifying cut off
>
>
>
> Are you using PME for your calculations?
>
>
>
> -michael
>
>
>
> On Apr 7, 2005, at 4:30 PM, Michel Espinoza-Fonseca wrote:
>
>
>
> Hi all,
>
>
>
> I have a technical question. Im running MD simulations of peptides to
> see the effect of phosphorylation. Originally I used a cutoff of 12 A,
> and now I changed it to 9 A. Interestingly, I obtained different
> results; for example, the unphosphorylated peptide remained more or
> less stable as a helix using the 12 A cutoff, while changing it to 9
> starts to unfold at around 5 ns. So Im wondering if anybody knows an
> article where the cutoff has been systematically modified, and how
> this cutoff (particularly using NAMD) affect the results of the
> simulation. Im really interested in that because certainly the effect
> of phosphorylation on the stability would be led by the electrostatic
> term in the system.
>
>
>
> Thank you very much!
>
>
>
> Cheers,
>
>
>
> Michel
>
>
>
> -----------------------------------------------------------------------
> ---------------------------
>
> Michael Grabe, Ph.D.
>
> HHMI/UCSF
>
> Genetics Development & Behavioral Science Building
>
> 1550 4th Street, GD 481
>
> San Francisco, CA 94143-0725
>
> tel: ++ 415.476.0421
>
> http://itsa.ucsf.edu/~mgrabe
>
>
>
>
>
------------------------------------------------------------------------
--------------------------
Michael Grabe, Ph.D.
HHMI/UCSF
Genetics Development & Behavioral Science Building
1550 4th Street, GD 481
San Francisco, CA 94143-0725
tel: ++ 415.476.0421
http://itsa.ucsf.edu/~mgrabe

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