[gmx-users] FW: dynamic of a peptide in a mixture TFE/H2O ( 30/70 %)

[Justin A. Lemkul]

Quoting Luisa Calvanese <luisacalvanese at hotmail.com>:

>
>
>
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> I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %).I'm using
> this file.mdp : cpp = /lib/cppdefine = -DFLEX_SPC -DPOSRESconstraints =
> all-bondsintegrator = mdtinit = 0.0dt = 0.002 ; ps !nsteps = 500000 ; total
> 1000 ps.nstcomm = 1nstxout = 1000nstvout = 1000nstfout = 0nstxtcout =
> 50xtc_precision = 1000nstlog = 1000nstenergy = 1000nstlist = 5rlist =
> 1.0coulombtype = Cut-offrcoulomb = 1.4rvdw = 1.4epsilon_r = 1.0; Temperature
> coupling is on in two groupsTcoupl = Berendsentc-grps = systemtau_t =
> 0.1ref_t = 300; Energy monitoringenergygrps = system; Pressure coupling is
> not onPcoupl = Berendsentau_p = 0.5compressibility = 4.5e-5ref_p = 1.0;
> Generate velocites is on at 300 K.gen_vel = nogen_temp = 300gen_seed = 173529
>   I 'd know if this file is correct.Thank you

Correct in what regard?  You've given us no sense of what you're trying to
accomplish, what force field you're using, etc.  Is the use of this .mdp file
generating some sort of problem?  If so, describe the error and perhaps someone
will have an idea.  Other than that, it's not our job to do your homework for
you.  Look up parameters in the literature for similar systems and for use with
your force field (i.e., rvdw, rcoulomb, etc.) and base your decisions off of
what you find.

-Justin

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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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