AMBER Archive (2007)

Subject: RE: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1

From: Jiapu.Zhang_at_csiro.au
Date: Mon Jan 29 2007 - 16:08:26 CST

Dear Ross,

 

Thank you very much for your helps.

 

Yes, I set irest=1 and ntx=7 in both input files, see:

 

 

md1_heat_A.in (start from the *.rst gotten at 300K):

Stage 1: 300K-400K and 400K-400K

 &cntrl

  imin = 0,

  irest = 1,

  ntx = 7,

  ntb = 1,

  cut = 12,

  ntr = 1,

  ntc = 2,

  ntf = 2,

  tempi = 300.0,

  temp0 = 400.0,

  ntt = 3,

  gamma_ln = 1.0,

  nstlim = 900000, dt = 0.0005,

  ntpr = 100, ntwx = 100, ntwr = 1000,

  nmropt = 1

 /

 &wt type='TEMP0', istep1=0, istep2=400000,

   value1=300.0, value2=400.0

 /

 &wt type='TEMP0', istep1=400001, istep2=900000,

   value1=400.0, value2=400.0

 /

 &wt type='END'

 /

Keep the protein restrained with weak restraints

10.0

RES 1 104

END

END

 

md1_heat_A_continuation.in:

Stage 1: 400K-400K

 &cntrl

  imin = 0,

  irest = 1,

  ntx = 7,

  ntb = 1,

  cut = 12,

  ntr = 1,

  ntc = 2,

  ntf = 2,

  temp0 = 400.0,

  ntt = 3,

  gamma_ln = 1.0,

  nstlim = 900000, dt = 0.0005,

  ntpr = 100, ntwx = 100, ntwr = 1000,

  nmropt = 1

 /

 &wt type='TEMP0', istep1=0, istep2=900000,

   value1=400.0, value2=400.0

 /

 &wt type='END'

 /

Keep the protein restrained with weak restraints

10.0

RES 1 104

END

END

 

In the second input file, I change ntt=3 into ntt=1 (with tautp=2.0),
the same RMSD-time graph thing - there is a small jump - happened!

 

By the way, could you please teach me how to choose the value of the
parameter gamma_ln for high temperatures such as 400K, 500K? gamma_ln
<=5.0, is it right? Then at 400K, gamma_ln=? and at 500K gamma_ln=?

 

Great thanks to you for your help.

 

Best regards,

Jiapu

 

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Ross Walker
Sent: Monday, 29 January 2007 5:17 PM
To: amber_at_scripps.edu
Subject: RE: AMBER: Why there is a gap or jump if continue ntt=3 or
ntt=1

 

Dear Jiapu,

 

Can you post the input files for phase I and II? Are you definately
restarting phase II from phase I? I.e. set irest=1 and ntx=5? Otherwise
you will get velocities reset and this will likely give you a jump in
kinetic energy which quickly feeds into potential energy and could
manifest itself as a small jump in RMSD.

 

All the best

Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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  _____

        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
On Behalf Of Jiapu.Zhang_at_csiro.au
        Sent: Sunday, January 28, 2007 22:05
        To: amber_at_scripps.edu
        Subject: AMBER: Why there is a gap or jump if continue ntt=3 or
ntt=1

        Dear Amber friends,

         

        Recently when I do equilibration, first the system was warmed up
from tempi to temp0, using ntt=3. I call it phase I. Then I want to do
further equilibration at temp0 (constant temperature now), during which
I still use ntt=3 (or use ntt=1). I call it phase II. All these two
phases are done under constant volume (i.e. ntb=1). However, when I draw
the RMSD-time graph of phase I and phase II, I always see there is a
gap, about 0.1 angstroms, between the RMSD of phase I and the RMSD of
phase II. This is not wanted by my theoretical think. Could someone
explain me why there is such a ugly jump for the RMSD? Thanks in
advance.

         

        Sincerely yours,

        Jiapu

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