Re: [gmx-users] Distance restraints exploding system

2013-09-05 Thread Trayder Thomas
To wrap this up for anyone who stumbles across this in the future: The 'solution' I ended up going with was to avoid using hydrogen atoms in the restraints, instead restraining to the e.g. methyl carbon and adding a fudge factor to the restraint length to account for the C-H distance. This results

Re: [gmx-users] Distance restraints exploding system

2013-09-02 Thread Rafael I. Silverman y de la Vega
Have you tried with even less restraints? I found systems are not always stable with more than the bare minimum of restraints On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas wrote: > It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have > an impact. I've tried being gentle,

Re: [gmx-users] Distance restraints exploding system

2013-09-01 Thread Trayder Thomas
It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have an impact. I've tried being gentle, slowly turning up the force constant and running for 1 ns for each value but as soon as the force constant approaches 100 it crashes. The starting structure was generated with the same re

Re: [gmx-users] Distance restraints exploding system

2013-08-30 Thread Mark Abraham
On Fri, Aug 30, 2013 at 8:56 AM, Trayder wrote: > Hello, > I am attempting to simulate a protein-ligand complex using distance > restraints to match it to NMR data. > The system runs stably without restraints. With restraints it tends to spit > out LINCS angle warnings and blow up under most condi

[gmx-users] Distance restraints exploding system

2013-08-29 Thread Trayder
Hello, I am attempting to simulate a protein-ligand complex using distance restraints to match it to NMR data. The system runs stably without restraints. With restraints it tends to spit out LINCS angle warnings and blow up under most conditions. I'm attempting to use: ; Restraints disre