[gmx-users] help

[Mark Abraham]

On 8/07/2011 1:31 PM, ÏþÓ¢ wrote:
> Hi,
> I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field 
> .I have done energy minimization .Then mdrun in NVT,but there is 
> always LINCS error .When I make impolicit_solvent=no,it can run 
> successfully. Is there a problem in the parameter settings? How can I 
> solve the problem?
> Step 49, time 0.049 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 56.816425, max 1019.791504 (between atoms 2943 and 2942)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2913 2912 90.1 0.1093 62.1434 0.1093
> 2920 2919 91.3 0.1093 4.7180 0.1093
> 2943 2942 90.1 0.1895 99.4251 0.0974
> Wrote pdb files with previous and current coordinates
> mdp file is in the attachment.
>
>

There's a few threads like this in the archives. Probably a smaller time 
step while equilibrating is in order.

Mark