On Apr 17, 2012, at 10:26 PM, Shulin Zhuang <shulin.zhuang.gmail.com> wrote:
> Dear All,
>
> I have routinely performed a 11 ns MD simulation in NPT ensemble based on
> X-ray crystal structure with a resolution of 1.87 angstrom . After the RMSD
> analysis, I found that the C alpha RMSD is continiously increasing and
> finally is is up to *5 Å*. The averaged RMSD for the* 0-1ns* simulation, *
> 1-6ns* simulation, *6-11ns* simulation is *2.3** Å, 2.86 Å, 3.89
> Å,*respectively. Attached
> is the RMSD figures.* It seems abnormal* and could you tell me where is the
> problem.
>
> The simulatioin input files were listed as following:
> *
> Minimization step 1 input:*
>
> restrained mimimization
>
> &cntrl
>
> imin=1, maxcyc=1000, ncyc=500, cut=10.0, ntb=1,
>
> ntr=1, restraintmask='(:268) & (!.H=)', restraint_wt=10.0
>
> # here 268 is the ligand. In this step, the ligand and non-hydrogen part of
> the system were restrained.
Your comment here is not correct. You restrained only the non-hydrogen parts of residue 268. You are selecting only atoms that are in residue 268 AND atoms that are not hydrogen. According to your comment, you want to use | (or) instead of & (and).
>
> /
>
> *Minimization step 2 input:*
>
> restrained mimimization
>
> &cntrl
>
> imin=1,maxcyc=1000, ncyc=500, cut=10.0, ntb=1, ntr=0,
>
> /
>
> *Heating stage input:*
>
> restrained heating process
>
> &cntrl
>
> imin=0, irest = 0, ntx = 1, ntb = 1, ntr = 1, ntc= 2, tempi = 0.0,
> temp0 = 300.0,
>
> ntt = 3, gamma_ln = 1.0, nstlim = 25000, dt = 0.002, ntpr = 100, ntwx
> = 500, ntwr = 500,
>
> cut=10.0, restraintmask='(:268) & (!.H=)', restraint_wt=5.0,
Same comment here with the restraint mask.
You can use ambmask to print out what each mask -really- selects.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 17 2012 - 20:30:05 PDT
