[gmx-users] NVT equilibration of ethanol in OPLSAA ff

[Mark Abraham]

On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote:
> Dear All,
>              I downloaded ethanol.pdb file from prodrg server 
> (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of 
> gromacs to create topology file for ethanol. I used genconf_d command 
> to generate solvent box of 512 molecules (as of Bevan's gromacs 
> tutorial) and then I scaled the solvent box for the density of ethanol 
> (785.22 g/l) at 298.15.

Did you view the system+box at this stage? What were your actual 
commands? You will get much more effective help if you provide an excess 
of information, than if you expect people to guess the right follow-up 
questions when they have little information.

> Before creatin solvent box I EM the isolated solvent molecule, then I 
> used that molecule to generate the solvent box. Then I EM the solvent 
> box 512 molecules.Followin are the parameters for EM of Solvent box.
>
> ; RUN CONTROL PARAMETERS
> integrator               = steep
> ; start time and timestep in ps
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 10000
> nstlist                  = 10
> rlist                    = 1.1
> coulombtype              = pme
> pme_order                = 4
> fourierspacing           = 0.16
> rcoulomb                 = 1.1
> vdw-type                 = cut-off
> rvdw                     = 1.1
> nstenergy                = 10
> ; ENERGY MINIMIZATION OPTIONS
> emtol                    = 1000.0
> emstep                   = 0.1
>
> I saw the em.xvg file it is minimized well.
> Then I started NVT equilibration with lincs constraints for hbonds at 
> timesteps of 0.2 fs and runned for 5 ps. The resultant configuration 
> shows that most of the molecules were together at region of box and 
> there was some void inside the box. I used cut-off of 1.1 nm for 
> electrostatic and VdW interactions. I didn't use any shift or switch 
> function. (can anybody suggest me a good tutorial to understand the 
> judicious use of this functions.)

What you've done is fine so far. There is no clear path for these 
choices. Ideally you should consider the scheme under which the force 
field was parameterized, and how it has been successfully used since, 
and do something very similar.

Mark

> Please help me sort this problem. If you need further details I am 
> ready to send you.
>
> Thank you.
>
> With Regards,
> Ravi Kumar Venkatraman,
> IPC Dept.,
> IISc, INDIA.
>
>
>
>
>

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