[gmx-users] REMD queries

rama david ramadavidgroup at gmail.com
Sat Oct 13 10:06:30 CEST 2012

Hi friends ,
                I am new to the REMD simulation.
I read some thread from archive but they not clarify by queries that why I
am asking you  on forum

 I have following Queries:

1.  I want to simulate protein by remd at physiological temp ( 310).

     So my initial temp of replica should be 310 or less than that???
2.  I read some thread for archive but not get the exact protocol :

       As per the   http://www.gromacs.org/Documentation/How-tos/REMD
link I have to do the seperate NVT for each replica...

But Should for NPT and Production run  I have to do the same thing ???

Or please help me to set the proper protocol..

When I used the T-remd      http://folding.bmc.uu.se/remd/

for NVT

*ERROR*: Can not do constant volume yet!

So how to determine temp for the nvt ???

Is it possible to run replica directly in the production run ???

These may be simple  question but as  new to REMD these question putting me
in a great trouble

For NPT with constrained I got following result

Summary of input and derived variables. VariableValue Pdes0.1 Temperature
range310 - 350 Number of water molecules3000 Number of protein
atoms284 Including
all H~ 431 Number of hydrogens in protein~ 62 Number of constraints~ 284 Number
of vsites~ 0 Number of degrees of freedom~ 27568Energy loss due to
constraints1.18 (kJ/mol K)

Should I have to use these same value for NVT and production MD ???

or for production MD I have to use NPT Constraints in the protein: fully

I just confused with these options.

So please give me proper protocol.

Thank you in advance.

With best wishes and regards
Rama david,

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