[gmx-users] Thank you, Erik and another question!

[Erik Lindahl]

Hi,

Just use the water value; almost all fluids are similar (at least  
within an order of magnitude).
Anyway, it won't affect the equilibrium properties of your system, just  
the rate of the fluctuations and equilibration.

To get the correct pressure it is a good idea to enable dispersion  
corrections.

Finally, once you start the simulation of the molecule you were  
building before, it is a good idea to check the energy in  
bonds/angles/dihedrals and make sure it equals about kT/2 per degree of  
freedom; if it is significantly higher for one of the terms it  
indicates your molecule is strained or cannot relax sufficiently  
(probably topology error).

Cheers,

Erik




On Sunday, Mar 2, 2003, at 20:15 US/Pacific, PeiQuan Chen wrote:

> Dear Erik：
>   Thank you for your kindly help!
>   Following your instruction and carefully reading the user manual,
> I have successfully creat the topology file for the molecule. And
> the result of the computation seems to be reasonable!
>    Thank you very much!
>
>    Now I have another question to ask you:
>    Recently I want to make a equilibriumed box(3.25878nm 3.25878nm
> 3.25878nm) contianing 216 CCl4 molecules.The density of the box is
> appoximatyl equal to the experimental data.
>    First,I build the box use genbox program,and do an energy
> miniziation on the box.
>    Second,I want to get the NVT and NPT ensemble molecular dynamics
> simulation to obtain the equilibriumed box.But I have  some trouble
> in define the compressibility. From the user manual,I know the value
> for water is 4.5e-5(1atm 300K). But the value of the CCl4 isn't
> listed in the manual. I want to ask how to define the value of CCl4
> (1atom 300K).
>
> Sincerely yours
> ----
> PeiQuan Chen
> _______________________________________________________________________ 
> _
> PeiQuan Chen 	Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone:	(86)2223506728		Mobile Phone: (+86)13920675030
> gromacs at 163.com	
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> +
>
>
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