[gmx-users] Re: Simluations in vacuum - energy increase

[David van der Spoel]

On 2011-05-01 20.00, Zoe Hall wrote:
> Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says "hbonds", not "h-bonds", however didn't make much difference which one I used. Could someone suggest the reason why you would want to turn temperature coupling off during the simulations - I don't really understand this.
>
In our work we want to study evaporation and cooling induced by the 
leaving water molecules. If you don't have water molecules, or even 
assume some kind of heat bath (e.g. a gas atmosphere), you could turn on 
T-coupling.
> Thanks,
>
> Zoe
>
> On 2011-04-30 14.17, Zoe Hall wrote:
>> Gmx-users,
>>
>> I am trying to carry out a simulation of lysozyme in vacuo using the
>> OPLS-AA forcefield. After energy minimisation, the protein is run for
>> 10ps with position restraints and temperature coupling on. This is
>> followed by the full production run of 10ns with temperature and
>> pressure coupling turned off, H bonds are constrained using LINCS and a
>> time step of 1fs. For vacuum conditions, the periodic boundary
>> conditions are turned off, and no cut-offs are used. When I carry out
>> the 10ns simulation the total energy gradually increases, as does the
>> temperature from 300 to 500K. I presume this is because the temperature
>> coupling is turned off, however that is what I have noted from the
>> literature that others do for their vacuum simulations. Can anyone shed
>> any light on this? Following is my method.
>>
>> integrator = md
>>
>> tinit = 0
>>
>> dt = 0.001
>>
>> nsteps = 10000000
>>
>> nstxout = 20000
>>
>> nstvout = 20000
>>
>> nstfout = 0
>>
>> nstlog = 100000
>>
>> nstenergy = 100000
>>
>> nstxtcout = 20000
>>
>> energygrps = Protein
>>
>> nstcomm = 5
>>
>> nstlist = 0
>>
>> ns-type = simple
>>
>> pbc = no
>>
>> rlist = 0
>>
>> coulombtype = Cut-off
>>
>> rcoulomb = 0
>>
>> epsilon_r = 2
>>
>> vdw-type = Cut-off
>>
>> rvdw =0
>>
>> Tcoupl = no
>>
>> tc-grps = Protein
>>
>> tau_t = 0.1
>>
>> ref_t = 300
>>
>> Pcoupl = no
>>
>> Pcoupltype = Isotropic
>>
>> tau_p = 1
>>
>> compressibility = 4.5e-5
>>
>> ref_p = 1.0
>>
>> gen_vel = yes ;
>>
>> gen_temp = 300.0
>>
>> gen_seed = -1
>>
>> constraints = hbonds
>>
>> constraint-algorithm = LINCS
>>
>> lincs_order = 4
>>
>> Thanks,
>>
>> Zoe
>>
>> Zoe Hall
>>
>> Department of Chemistry
>>
>> Oxford University
>>
>> _zoe.hall at chem.ox.ac.uk_
>>
> Are you sure h-bonds are being constrained, because otherwise the time
> step is too large? (maybe you need to write h-bonds). You may need to
> increase the constraint accuracy as well. We did all our vacuum calcs in
> double precision as well IIRC.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se