if you haven't already done this, I suggest (1) making sure MD without the
tgtmd works fine using the same input coordinates and (2) try the tgtmd
using sander with a single CPU and shorter nstlim, with ntpr=1 so you can
get a better idea of whether something is wrong with the energies. also,
what is your reference coordinate set?
On Mon, Dec 22, 2014 at 8:31 AM, antonio.coluccia.uniroma1.it <
antonio.coluccia.uniroma1.it> wrote:
>
> Dear All,
> I would like to carry out a target dynamics.
> Following suggestion fro the mailing list
> i have computed parameters for starting and reference conformations of
> studied protein with leap,
> checked the number of atoms and computed the minimization for both
> conformations.
> When i use sander to carry out target dynamics calculation the system
> was frozen at the step 0 with the RMSD higher that the real one and with
> CPU working at 100%.
> I suppose that the problem could be the size of the water boxes for the
> two protein conformations
> but i do not know how to solve the problem
> Do you have any suggestions?
>
> My input file is:
> &cntrl
> nstlim= 10000000, dt=0.002, temp0=300.0, ntt=1,
> ntpr=500, ntwr=5000, ntwx=5000,
> ntx=1, ntpr=100,
> ntf=1, ntc=1, ntb=0,
> igb=1, gbsa=0,
> nsnb=25,
> itgtmd=1, tgtmdfrc=10,
> tgtfitmask=":1-674.CA,N,C,O",
> tgtrmsmask=":1-674.CA,N,C,O",
>
> &end
> &wt type='TGTRMSD', istep1=1, istep2=10000000, value1=2.00 , value2=0.0,
> > &end
>
>
> Any help will be really appreciated.
>
> with best regards
>
> Antonio
>
> --
> Antonio Coluccia, Ph.D.
> Department of Chemistry and Drugs Tecnology
> La Sapienza University
> Rome 00185
> Piazzale Aldo Moro 5
> antonio.coluccia.uniroma1.it
> mobile: 00393406113351
>
>
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Received on Mon Dec 22 2014 - 06:00:07 PST
