Vaibhav,
AMBER does not compute pressure, volume, or density unless they are needed
for dynamics (*i.e. *ntp > 0). The zeros you are seeing are just place
fillers.
The ntb flag, to my knowledge, is now deprecated and should be set
automatically based on the barostat options and box information (I
*think*from the inpcrd only, but I could be wrong).
Regards,
Brian
On Mon, Apr 22, 2013 at 3:43 AM, Vaibhav Dixit <vaibs1.gmail.com> wrote:
> Hello,
>
> I am new to MD simulations using AMBER. I want to know what should be the
> paramteres in input files for running a NVT simulation in AMBER.
> Is this ok?
>
> polyA-polyT 10-mer: 100ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 50000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
>
> This lead to the pressure being zero everytime in simulation. Is it
> accepted? Or should I put give any values to NTP, pres0 ?
>
> thanks in advance!
>
> --
> *Vaibhav Dixit
> *
> *Undergraduate Student*
> *Chemical Science and Technology*
> *Indian Institute of Technology Guwahati,India*
> *
> *
> *Alt Email: v.dixit.iitg.ac.in*
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
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Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Mon Apr 22 2013 - 06:00:06 PDT
