RE: modifying cut off

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Apr 07 2005 - 19:45:30 CDT

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Thank you for your reply Michael. I also knew that using PME there is no
truncation of the electrostatics. I was wondering because I'm using
multiple time stepping, so I'm treating the long range electrostatic
term. As I mentioned, now I'm obtaining the results I want to obtain,
but I wanted to know if there is any systematic analysis about this (I
mean, modifying the cutoff)... Anyway, I have to wait for the full
results (phosphorylated and unphosphorylated) and then I'll see...

Again, thank you for your reply!

Cheers,

Michel

________________________________

From: Michael Grabe [mailto:mgrabe_at_itsa.ucsf.edu]
Sent: Thursday, April 07, 2005 7:38 PM
To: Michel Espinoza-Fonseca
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: modifying cut off

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. I'm 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 I'm 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. I'm 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

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Michael Grabe, Ph.D.

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