Thanks RADAK. I have prepared a input file as follows:
test of umbrella sampling of two distance
&cntrl
nstlim=50000,
cut=10.0,
ntpr=100, ntwr=200, ntwx=100
ntt=3, gamma_ln=1.2,
ntx=7, irest=1,
dt=0.001, ntb=1,
nmropt=1,
/
&wt type=’DUMPFREQ’, istep1=10 /
&wt type=’END’ /
DISANG=dist1.RST
DISANG=dist2.RST
DUMPAVE=set1.dat
I am confused how to write the corresponding RST file. As I mentioned before I want to increase a bond length (between 12231 and 12248) gradually and decrease another bond length (between 12248 and 9887). The following is the corresponding RST file,
dist1.RST
&rst iat=12231, 12248, r1=1, r2=1.5, r3=1.5, r4=2, rk2=1000.0, rk3=1000.0
dist2.RST
&rst iat=9887, 12248, r1=3.5, r2=3.0, r3=3.0, r4=2.5, rk2=1000.0, rk3=1000.0
is it correct?
It is not clear to me that what is the r1, r2, r3 and r4. Will you plz explain me.
with regards
sindrila
________________________________
From: Brian Radak <radak004.umn.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 8 February 2013 11:37 PM
Subject: Re: [AMBER] Problem related to the umbrella sampling
Sindrila,
Please don't double post to the list.
(i) It's certainly possible that the starting structure is thermodynamically unfavorable given the sampling potential (i.e. with restraints). Whether or not this is "correct" is pretty much up to the user.
MM force fields are usually robust enough to quickly relax to a more plausible configuration while QM/MM potentials are often inclined to fail gloriously and predict chemistry never before known to man. Personally, I would recommend, at the very least, inspecting several (or all) of the trajectories at the outset to verify that they look "correct" to you.
(ii) All AMBER nmropt restraints are read from &rst namelists in the file specified by DISANG. To add multiple restraints simply add additional namelists. This should be well documented in the manual.
(iii) I am not sure what you mean here. I think the answer to (i) above covers this as the starting structure is the starting structure, regardless of how it is generated. One might be able to make subjective arguments about how "correct" a starting structure is, but this is essentially left to the user.
That being said, you may certainly get completely different results depending on the equilibration protocol that goes into generating the starting structure. If you are performing a 1d umbrella sampling, I have occasionally found it useful to use the "jar" option to slowly change the potential in a non-equilibrium fashion. Presumably if the driving rate is not too fast (that is meant to be as ambiguous as it sounds) then the equilibrium of the starting structure is minimally perturbed and it should be "correct".
Regards,
Brian
On Fri, Feb 8, 2013 at 12:30 PM, Sindrila Dutta banik <sindrila.duttabanik.yahoo.com> wrote:
Dear all,
>In the manual for the umbrella sampling an example is given for a torsional angle restrain.
>As I understood from the manual
>and tutorial that first I have to generate different windows (having
>different angle value), then for each window minimize, equilibrate,
>production run with saving DUMPAVE. Then from this files generate the PMF.
>
>Now I want to know
>(i) If I apply a restrain by DISANG command it will create a strained
>structure. Is it correct?
>(ii) How to apply two restrain simultaneously? what should be TYPE for this? DISTANCE? (iii) Is it possible to apply restrain gradually?
>(iv) If I apply restrain gradually then also I have to perform
>equilibrate, production run?
>
>With best regards
>Sindrila
>_______________________________________________
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>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State University of New Jersey
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Department of Chemistry : Piscataway, NJ 08854-8066
radak004.umn.edu : radakb.biomaps.rutgers.edu
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Received on Fri Feb 08 2013 - 12:00:02 PST
