Re: [AMBER] Lambda Exchange

From: Jeff Wereszczynski <>
Date: Wed, 8 Oct 2014 12:23:22 -0500

Hi Jason,

Thanks for your response. To follow up:

1. I can surely edit the prmtop files as you suggest. After I sent this
email it occurred to me that this will of course modify not only the
inter-molecular electrostatics, but also the intra-molecular
electrostatics. Is there a straightforward way to keep the intra-molecular
electrostatics on while scaling the energy terms between the ligand and the
rest of the system?

2. You said "to use softcore TI," however I can't use the normal TI
commands with H-REMD (this is the root of most of my issues). When I try
to do this, I get the following error:

| ERROR: TI is incompatible with REMD

For the record, my command line is:

mpirun -np 8 $AMBERHOME/bin/pmemd.MPI -ng 2 -groupfile groupfile -rem 3

the groupfile is:

-O -i mdin/ -o mdout/run.0.00.2.out -c
restart/run.0.00.10.rst7 -r restart/run.0.00.2.rst7 -x traj/
-e energy/run.0.00.2.ene -p charge_nocharge.prmtop -inf info/
-O -i mdin/ -o mdout/run.0.10.2.out -c restart/run.0.10.1.rst7
-r restart/run.0.10.2.rst7 -x traj/ -e energy/run.0.10.2.ene
-p charge_nocharge.prmtop -inf info/

and the relevant part of the first input file is:

        timask1=':149-157', timask2=':158-166',
        icfe = 1,
        clambda = 0.00,
        ifmbar = 1, bar_intervall=100,

And for the second input file it is:

        timask1=':149-157', timask2=':158-166',
        icfe = 1,
        clambda = 0.10,
        ifmbar = 1, bar_intervall=100,

Am I doing something wrong here? It looks to me like icfe is incompatible
with H-REMD in the current code, hence the needing a new prmtop file for
each lambda value. It isnt obvious to me if there is a way to specify
softcores in the prmtop since they change the functional form of the

3. For mbar, this comes back to the issue I had before with icfe not
working with "rem 3." If icfe is disabled none of the mbar commands work:

| ERROR: MBAR requires a standard TI run, set icfe to 1

There may be something straightforward I'm missing here about my


Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology
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Received on Wed Oct 08 2014 - 10:30:02 PDT
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