Re: [AMBER] HMassRepartition

From: Thakur, Abhishek <>
Date: Wed, 16 Nov 2016 15:55:45 +0000

Elvis thank you for such a quick response I am using default value for gama_ln. so I guess it must be 0. Do you suggest someother value that I should define>

David I don't think that I am using ig=-1, do you recommend me to try with that?

This is the script I am using in both case,

Just with the difference of time step

  ntpr=500, ntwx=500, ntwr=10000,

From: David Cerutti <>
Sent: Wednesday, November 16, 2016 4:46:06 AM
To: AMBER Mailing List
Subject: Re: [AMBER] HMassRepartition

These are both very short runs, and without knowing any other details
(assuming you have done everything correctly) I would expect the dimer to
open with 1fs time steps soon enough. Just to make sure, are you running
with a clock-based or otherwise varying random seed? I don't know what the
status of all our bulletproofing is, but if you're running with ascii
restarts then there could still be a way to get repeating pseudo-random
sequences into your system which would tend to unfold proteins if the
restarts occur frequently enough (or cause milder "opening" effects if the
restarts happen less frequently).


On Wed, Nov 16, 2016 at 10:38 AM, Thakur, Abhishek <> wrote:

> Hi,
> I have carried out two different GB/SA simulation, igb=5 and all the
> parameters same
> 1. With HMassRepartition with dt=0.004 and in 20ns I found that my dimer
> opened.
> 2.Simple Gb/SA with dt=0.001 and in 20ns I have found my dimer has not
> moved at all.
> I cannot get the reason behind this, as both have same duration of
> simulation. Can this be possible or I have done some mistake>
> Thanking you,
> Abhishek
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Received on Wed Nov 16 2016 - 08:00:05 PST
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