[gmx-users] Re: NEMD

[Junqiao Lee]

I'm currently using Gromacs 4.5.1
My system is stable up to 490K before it blows up under normal MD.
Cheers, Jun (Wade)

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

> 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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