AMBER: Targeted MD

From: Whitney Allen <>
Date: Thu, 20 Oct 2005 11:04:31 -0700 (PDT)

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 ( 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



cat <<eof > mdin

  equilibrate the structure


   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,


Group for target

RES 1 76





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 - 19:53:00 PDT
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