On 1/15/2013 7:58 AM, David A Case wrote:
> On Mon, Jan 14, 2013, Kirill Nuzhdin wrote:
>> 1. How to set density for periodic system? Just by changing the size of
>> the box at the end of a coordinate file?
> Generally, one runs constant pressure simulations (at least during
> equilibration) so that the density is adjusted to be that the force field
> wants for the given external pressure.
>
> You can indeed adjust the density by hand by chaning the box dimensions, but
> if you made the box smaller than the actual dimensions of the atoms inside it,
> you would get terrible overlaps that would probably crash the simulation.
Is it possible to run MD without LES but with q-spcfw force field? I
have this question because my PBC system keeps exploding with ntb = 1
and with ntb = 2
Input files are -
for const volume:
ntb = 1, ig = -1, ntx = 1, irest = 0, jfastw = 4, ntc = 1,
ntf = 1
temp0 = 300.0, ntt = 3, gamma_ln = 5.0, dt = 0.0002, nstlim =
50000, cut = 7.0
ntpr = 50, ntwr = 50, ntwx = 50
for const press (same +):
ntb = 2, ntp = 1, pres0 = 1.0, taup = 20.0
>> 3. addles is failing with the following error:
>> ---------------
>> LES was applied to solvent, atom 34
>> This is not allowed.
>> ---------------
>> Why is it not allowed?
> This check is not applied if you are using LES to create pimd (path integral
> MD) input. So it looks like your input to addles is missing the "pimd"
> option(?).
I'm not sure I understand what you mean by "using LES to create pimd"?
As per manual: I used regular topology and coord. files and created
addles.in script for addles.
--
Best regards,
Kirill Nuzhdin
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Received on Tue Jan 15 2013 - 15:30:02 PST
