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

[PeiQuan Chen]

Dear Erik：
  To make a equilibrium box(3.25878nm 3.25878nm 3.25878nm) that 
contianing 216 CCl4 molecules. First I must build the CCl4 topology
file. And I want to make a oplsaa model of CCl4. From the instruction
of you ever told, I would better to make the topology file using the 
pdb2gmx program. So I have to built the block of CCl4 in the 
ffoplsaa.rtp. From the G43.rtp file. I get the rtp entry for the CCl4,
I have something Uncertain of the block.

In the G43.rtp file:
[ CCL4 ]
 [ atoms ]
    CCl4  CCL4     0.00000     0
    CLCl1 CLCL4    0.00000     0
    CLCl2 CLCL4    0.00000     0
    CLCl3 CLCL4    0.00000     0
    CLCl4 CLCL4    0.00000     0
 [ bonds ]
    CCl4 CLCl1    gb_40   
    CCl4 CLCl2    gb_40   
    CCl4 CLCl3    gb_40   
    CCl4 CLCl4    gb_40   
    CLCl1 CLCl2    gb_47   
    CLCl1 CLCl3    gb_47   
    CLCl1 CLCl4    gb_47   
    CLCl2 CLCl3    gb_47   
    CLCl2 CLCl4    gb_47

For example, the CLCl1 atom and CLC2 atom isn't bonded. Why in these 
files, It consider them bonded??

If I want to get the oplsaa model CCl4 topology file, isn't this block
entry suitable for me?  If yes, How can I find the parameters of the 
Cl-Cl and Cl-Cl-CT etc.? If no, How can I build the block for CCl4?

>To get the correct pressure it is a good idea to enable dispersion  
>corrections.
Which option of the DispCorr should I use? EnerPres and Ener?

Thank you in advance!

>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



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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