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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Ross Walker
Sent: Monday, 29 January 2007 5:17 PM
To: amber.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
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk <
http://www.rosswalker.co.uk/> | PGP Key
available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may
not be read every day, and should not be used for urgent or sensitive
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_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu]
On Behalf Of Jiapu.Zhang.csiro.au
Sent: Sunday, January 28, 2007 22:05
To: amber.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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Received on Wed Jan 31 2007 - 06:07:26 PST
