Dear Amber users,
I am currently planing to use temperature based REMD
for my work. For this I am learning the application following the REMD
tutorial mentioned in the Amber tutorial
http://ambermd.org/tutorials/advanced/tutorial7/.
I have few queries and will be glad if you can kindly give me your input.
1) The first is regarding the chirality restraints. I am planing to
use the temperature range between 300-400K for my study. I have done a
search of the mailing list and came across threads
(
http://archive.ambermd.org/200901/0203.html) where it was mentioned
that for this range of temperature, it is not critical to have the
chirality restraint. So I am planing to not use it for my study. Is
this a fair judgment?
2)In the REMD tutorial of Amber, there is an equilibration run
performed for all the replicas before actually doing REMD. Now in the
step after the equilibration, the authors have given an example of the
REMD.mdin (
http://ambermd.org/tutorials/advanced/tutorial7/). I am
just appending the parameters from the input file that is bothering me
below.
irest=0, ntx=1,
temp0=XXXXX, ig=RANDOM_NUMBER,
REMD uses the restart file from the equilibration run. So shouldn't it
be that irest=1 and ntx=5 so that the velocity information is also
read from the restart file?
And why are the authors setting the random number and initial
temperature again for the REMD run of the tutorial when the
temperatures are already set in the previous equilibration run?
3) I also have a query on the "ig" parameter. In the classical MD,
"ig=-1" is now routinely set in the input parameter file. Shouldn't it
be the case also for REMD simulations?
I am sorry for this long email and please excuse me if I have missed
something in my understanding of the concept.
I will be glad if you can give me an insight to the queries.
Thank you,
Dilraj.
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Received on Fri May 11 2012 - 00:30:04 PDT
