[gmx-users] Simulation in vacuum
Alex
nedomacho at gmail.com
Sun Jan 22 07:57:44 CET 2017
These errors are pretty much telling you what to do. For instance, set:
nstlist = 20
pbc = xyz
This is a pretty curious mdp file... Vacuum + NVE + constraints. I hope
you're not simulating a crystal this way.
Alex
On 1/21/2017 10:53 PM, Мижээ Батсайхан wrote:
> Dear Erik,
>
> Thank you very much for helping me.
> I have got 2 errors from grompp using gromacs v5.1.
>
> ERROR 1 [file nve.mdp]:
> With Verlet lists only full pbc or pbc=xy with walls is supported
>
> ERROR 2 [file nve.mdp]:
> With Verlet lists nstlist should be larger than 0
>
> How can I fix these? I copied my mdp file.
>
> #############################################
> title = NVE equilibration
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 100000000 ; 1 * 100000000 fs= 100000 ps = 100 ns
> dt = 0.001 ; 1 fs
> ; mode for center of mass motion removal
> comm-mode = Angular
>
> ; Output control
> nstxout = 5000
> nstvout = 5000
> nstenergy = 5000
> nstlog = 500
> ;energygrps =
>
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = hbonds
> lincs_iter = 2
> lincs_order = 4
>
> ; Neighborsearching PARAMETERS
> vdw-type = cut-off
> verlet-buffer-tolerance = -1
> rlist = 1
> nstlist = 0
> ns_type = grid
> pbc = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype = cut-off
> rcoulomb-switch = 0
> rcoulomb = 0.0
> rvdw = 0.0
> rvdw-switch = 0.0
> fourierspacing = 0.16
> epsilon_r = 1
> epsilon_rf = 78
> ; EWALD/PME/PPPM parameters
> pme_order = 4 ; cubic interpolation
>
> ; Temperature coupling
> tcoupl = no
> ;tc-grps =
> ;tau_t = 0.1
> ;ref_t = 300
> ; Pressure coupling
> pcoupl = no ; no pressure coupling in NVT
> ; Dispersion correction
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
> ################################################################
>
>
>
>
> Best regards,
> Mijiddorj
>
>> ------------------------------
>>> Message: 4
>>> Date: Fri, 20 Jan 2017 10:30:59 +0000
>>> From: Erik Marklund <erik.marklund at kemi.uu.se>
>>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>>> Subject: Re: [gmx-users] Simulation in vacuum
>>> Message-ID: <7745284C-EA36-4189-80A6-0A6AB4986FDC at kemi.uu.se>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Dear Mijiddorj,
>>>
>>> We have had good energy conservation with bond constraints and a 1 fs
>> time
>>> step under double precision, using a setup similar to yours. We did not
>>> remove rotation however, because we wanted to honour the rotational
>>> temperature of the system. Whether that is an important choice or not is
>>> for you to decide, but do note that the spinning ice cube effect is an
>>> artefact arising from the thermostat, which is turned off in your setup.
>>>
>>> Whether bonds should be constrained or not is related to what your
>>> scientific questions are, and the time step depends on what bonds are
>>> constrained, if any. I can?t remember what LINCS parameters we used, but
>> be
>>> prepared to increase the order and/or iter. Consult the manual for
>> details.
>>> Kind regards,
>>> Erik
>>>
>>> ______________________________
>>> Erik Marklund, PhD
>>> Marie Sk?odowska Curie INCA Fellow
>>> Department of Chemistry ? BMC
>>> Uppsala Universtity
>>> erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
>>>
>>> On 20 Jan 2017, at 11:01, ????? ????????? <b.mijiddorj at gmail.com<mailto:
>>> b.mijiddorj at gmail.com>> wrote:
>>>
>>> Dear gmx users,
>>>
>>> I would like to get experience of simulation in vacuum. Please suggest me
>>> tutorials, and advice me.
>>>
>>> I read about following comments which written on Shourjiya Sanyal
>> tutorial.
>>> Can you discuss about it?
>>>
>>> In vacuum simulation, integration should be reduced compared to solvent
>>> phase simulation. Periodic boundary conditions, non-bonded interaction
>>> cutoffs, temperature coupling and pressure coupling were all turned off.
>>> Center of mass translation and rotation around the center of mass are to
>> be
>>> removed to avoid the fast spin of the protein. One should also constrain
>>> the hydrogen bond using algorithms like SHAKE/LINCS.
>>>
>>> http://www.shourjya.thinkbiosolution.com/md-
>> simulation-in-gas-phasevacuum-
>>> with-gromacs/
>>>
>>>
>>> Best regards,
>>> Mijiddorj
>>> --
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