[gmx-users] Fwd: dmso

[Erik Lindahl]

Hi,

I got this from John Dalmaris yesterday; if you have any comments you 
might want to cc him on john.dalmaris at imperial.ac.uk since he's not 
subscribed to the list.

Cheers,

Erik
 
>
> I am not a member of the list so my attempt to send the following 
> message failed. I tried to send this e-mail to the gromacs users 
> because they have experience concerning my query. Since all of my 
> attempts to find an answer to this question did not work out I would 
> be obliged if you could circulate it to your members in anticipation 
> of any help.
>
>  
>
> I would like to apologise for any inconvenience caused.
>
>  
>
> Best wishes,
>
>  
>
> John
>
>  
>
>  
>
> Hello gromacs Users,
>
>  
>
> I am facing some problems with the DMSO box I am trying to set up (in 
> amber7) and I would like to verify the DMSO parameters I am using. I 
> have noticed that is a standard solvent in gromacs and I would 
> appreciate it if you could give me some feedback with respect to the 
> following parameters.
>
>  
>
> DMSO parameters file
> MASS
> CT 12.01
> S  32.06
> H1 1.008
> O  15.99
>
> BOND
> S-O   570.0   1.53
> CT-S  227.0   1.81
> CT-H1 340.0   1.09
>
> ANGL
> H1-CT-S    50.0   109.5
> CT-S-CT    62.0   97.4
> O-S-CT     80.0   106.75
> H1-CT-H1   35.0   109.50
>
> DIHEDR
> X-S-CT-X    0.85    3     0.0
>
> NONB
>  S  2.0000   0.2500
>  CT 1.9080   0.1094
>  O  1.6612   0.2100
>  H1 1.3870   0.0157
>  
>
>  
>
> I am concerned about the Dihedral parameters and I would like to ask 
> what are the parameters you are using for the dihedrals.
>
>  
>
> Many thanks for your help.
>
>  
>
> Best wishes,
>
>  
>
> John
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