Hi Steve,
I'll just address the first part of your reply...
On Jun 24, 2010, at 11:14 AM, Steve Seibold wrote:
> Hi Jason
> Thanks for your response/help.
>
>> We would need to see your input file that you used. I'm guessing
>> you did not specify ntwx (which is a number that specifies the
>> interval of snapshots that is saved to the trajectory file)
>
>> in your &cntrl namelist, which defaults to a value of 0. This means
>> that coordinates are never written to the mdcrd, even though you
>> may specify (-x test.mdcrd) on the command-line.
>
> Here is my input file for SANDER (my command line does have -x
> file.mdcrd):
>
>
> &cntrl
>
> ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 5, ntwx = 5000, ntwv = 0, ntwe = 50,
> ntwr = -5000,
>
> ntf = 1, ntb = 1,
> cut = 8.0, nsnb = 5,
>
> ibelly = 0, ntr = 0, nmropt = 0,
>
> imin = 0,
> nstlim = 10,
> nscm = 1000,
> t = 0.0, dt = 0.002,
>
> temp0 = 300.0, tempi = 300.0,
> ig = 71277,
> ntt = 1,
> tautp = 0.2,
> vlimit = 15.0,
> restraintmask= ':1-2495'
> restraint_wt =0,
>
> ntp = 0, pres0 = 1.0, comp = 44.6,
> taup = 0.2,
>
> ntc = 2, tol = 0.00001,
> lastrst = 8000000,
>
> &end
>
>
>
> So, I am not sure why SANDER is not writing out the md trajectory
> files.
>
> ---------------------------------------------------------------------------------
You have nstlim = 10, but ntwx = 5000 -- your simulation is running
for only 10 steps, but you are telling it to save out the trajectory
only every 5000 steps. Either make nstlim larger or ntwx smaller and
you should see some trajectory output.
You also have a number of other bits of code in there that might be
causing trouble:
(1) "ntxo = 0" -- this option (unformatted restart files) is no longer
supported in AMBER 11...at least according to the manual and several e-
mails from Prof. Case (though I think many of us agree that they would
useful).
(2) "ntwr = -5000" -- why the minus sign?
(3) "nsnb = 5" -- is there any reason for this? By default, sander
will update the nonbonded list automatically whenever any atom has
moved more than 0.5*skinnb since the last update.
(4) "lastrst = 8000000" -- this may no longer be supported in AMBER
11, as I don't see anything in the manual for this.
Best,
Paul
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Received on Thu Jun 24 2010 - 12:00:03 PDT
