Re: AMBER: Targeted MD

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Thu, 20 Oct 2005 14:31:21 -0400

it's hard to interpret this without seeing the mdout.
what is the initial target and actual rmsd and restraint energy? is it high?
this can also lead to vlimit erros (if the initial rmsd is far
from the target value).

Whitney Allen wrote:

> Hi Amber users
>
> I am trying to run Targeted MD on Amber, but I am getting some strange
> oscillatory behavior in the "current RMSD from reference values".
> Basically the plot looks almost exactly like an underdamped system
> going to the tgtrmsd value (thus it gets within the target rmsd, then
> moves away from it, goes back to near the target rmsd, then moves
> away, .). Below is an example of one of the files I am running
> (eq.in). I have adjusted the tgtrmsd value (1-4), tgtmdfrc value
> (0.005-1), nstlim (up to 2ns), and used different target/reference
> structures. All give the same behavior (which is also easily seen by
> viewing the trajectory). Second, depending on what reference structure
> I target, sometimes I get a vlimit exceeded error. What does this mean
> and how do I get rid of this? There is little documentation on
> Targeted MD so please help. Thanks in advance and let me know if I
> should send my files.
>
> Whitney Hastings
>
> (/eq.in/)
>
> cat <<eof > mdin
>
> equilibrate the structure
>
> &cntrl
>
> imin=0, ntx=5,
>
> irest=1, ntxo=1,cut=15.0, tempi=300.0,
>
> ntpr=10, ntwx=10, ntwe=1000,
>
> nstlim=100000,tautp=2, temp0=300.0,
>
> dt=0.001, nscm=100,
>
> igb=1,ntb=0, saltcon=0.5, gbsa=1,
>
> ntt=1, nsnb=20,offset=0.13,
>
> itgtmd=1, tgtrmsd=2.0, tgtmdfrc=0.1,
>
> &end
>
> Group for target
>
> RES 1 76
>
> END
>
> END
>
> eof
>
> mpirun -np 2 sander -O \
>
> -i mdin \
>
> -o eq.out \
>
> -p N218_0.prmtop \
>
> -c cst01.restrt \
>
> -ref min70.restrt\
>
> -r eq.restrt \
>
> -x eq.x
>
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Received on Thu Oct 20 2005 - 19:53:01 PDT
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