[gmx-users] Re: NEMD

[Junqiao Lee]

Hi Mark,

Yes my starting configuration is stable under normal MD.

I've since reduced cos_acceleration to 0.01 (nm ps^-2).
It seems to be holding together, however both *2CosZ*Vel-X* and *1/Viscosity
* that I've got out of the test runs (with the *g_energy* program) remained
at the value of 0 (as before). Perhaps I'll still need to specify something
else that I might have missed, which I can't seem to find in the manual
(still flipping through)?

I've included my run-input parameters below in-case that'll be helpful. =)

Thanks heaps for the help!

---------------------------------

integrator               = md
dt                       = 0.002
nsteps                   = 100000
comm-mode                = Linear
nstcomm                  = 10
nstxout                  = 10000
nstvout                  = 10000
nstfout                  = 0
nstlog                   = 500
nstcalcenergy    = 250
nstenergy                = 500
nstxtcout                = 500
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
coulombtype              = pme
rlist                    = 1.0
rcoulomb                 = 1.0
vdw-type                 = Cut-off
rvdw                     = 1.0
pcoupl                   = Parrinello-Rahman
pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 0.5
Tcoupl                   = v-rescale
tc_grps                  = System
tau_t                    = 0.1
ref_t                    = 298
gen_vel                  = no
gen_seed                 = 94839
constraints              = All-bonds
constraint-algorithm     = lincs

; acc_grps = MMA1 MMA53 MMA97 MMA123 MMA167 MMA197 MMA227
accelerate = 0.1
cos_acceleration = 0.01


Cheers
Jun (Wade)

On 14/11/2010 2:42 AM, Junqiao Lee wrote:
> Running the simulation in NVT doesn't seem to work too.
> And (other than the system not blowing up now) similar to the NPT
> simulations, both 2CosZ*Vel-X and 1/Viscosity that I've got out of the
> test runs were 0.

Is the starting configuration stable under normal MD?

Mark

On Sat, Nov 13, 2010 at 11:42 PM, Junqiao Lee <aeondrift at gmail.com> wrote:

> Running the simulation in NVT doesn't seem to work too.
> And (other than the system not blowing up now) similar to the NPT
> simulations, both 2CosZ*Vel-X and 1/Viscosity that I've got out of the test
> runs were 0.
>
> On Sat, Nov 13, 2010 at 11:17 PM, Junqiao Lee <aeondrift at gmail.com> wrote:
>
>> Hi,
>>
>> I've tried running an NEMD run in NPT vis setting the "cos_acceleration =
>> 0.3" parameter to determine the solvent viscosity.
>> However my system kept spectacularly exploding.
>> I've also tried running with the acc_grps specified for 7 molecules (out
>> of the 250 within the system), but it still didn't work.
>> cos_acceleration = ~0.3 nm ps^-2 seem like a reasonable value to use?
>> Am I only restricted to running NEMD calcs. in NVT?
>> Thanks for the help.
>> Cheers,
>> Junqiao LEE (Wade)
>> Curtin University
>> Dept. of Chem. [NRI]
>>
>
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