AMBER: how can I deal with the puzzle?

From: hj zou <>
Date: Wed, 9 Mar 2005 11:36:39 +0800

Hi, amber community,

        I have two conformations of a protein which have a RMSD of 440 angstrom.. I want to transfor from one conformation to another. In the simulation, I am confused that My simulation seems not be right in the process of targeted MD. There are several puzzles in my simulations as follows:
1. Could you tell me the parameters I used in the targeted MD is right?
targeted MD
         imin=0, nstlim=10000, dt=0.0005,
        ntx=5, ntt=1, npscal=1,
        ntc=2, ntf=2, ntb=2,
        ntpr=10, scee=1.2, cut=25,
        igb=0, irest=1, nmropt=1,
        lastist = 3500000,lastrst = 5000000,
        itgtmd=1, tgtrmsd=0.0, tgtmdfrc=0.5,
        TYPE='TGTRMSD', istep1 =1, istep2 = 1000,
        value1 = 441.2, value2 = 440.,
group input- define atoms for targeted md
CA * * *
N * * *
C * * *
O * * *
H * * *
HA * * *
RES 1 446
2.And In the output file, I found the temperature increased from 300K to 320K during 10000 steps, the whole energy was increased from negative value to positive. is it right?
3.Should I use the Born model(igb=1) for targeted MD?

I am greatly appreciated your reply, and Thank you in advance

Best regards,
Jian Zhang
Center for Drug Discovery and Design
Shanghai Institute of Materia Medica
Chinese Academy of Sciences
555 Zu Chong Zhi Road
Shanghai 201203, China
Tel: +86-21-50806600-1201(ext)


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Received on Wed Mar 09 2005 - 03:53:00 PST
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