[gmx-users] Re: NEMD

[Junqiao Lee]

Woops, btw please ignore the lines:
; acc_grps = MMA1 MMA53 MMA97 MMA123 MMA167 MMA197 MMA227
accelerate = 0.1
in the parameters pasted earlier.

They were not present in my initial test-runs. I was just trying out
alternatives...


On Sun, Nov 14, 2010 at 12:13 AM, Junqiao Lee <aeondrift at gmail.com> wrote:

> 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
>
>
> 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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