Re: [gmx-users] MD simulation of protein-protein complex

2013-02-21 Thread Justin Lemkul
On 2/21/13 10:18 AM, shahid nayeem wrote: Dear all I want to simulate a protein complex with 4 chains two of which is linked with disulfide bonds. Does this simulation requires that all chains are merged into one molecule definition or I should merge only two chains which are linked with disulf

Re: [gmx-users] "MD simulation of protein-protein complex"

2010-08-17 Thread XAvier Periole
That means that in your starting conformation you have strong forces probably coming from back contacts. minimization/equilibration should help removing them. On Aug 17, 2010, at 12:29 PM, rekkha nivethitha wrote: Hi frnds, On running, Molecular dynamics simulation of protein-protein compl

[gmx-users] "MD simulation of protein-protein complex"

2010-08-17 Thread rekkha nivethitha
*Hi frnds, On running, Molecular dynamics simulation of protein-protein complex, While running md run, i got this error, * "Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5# Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5# Step 0, time 0 (ps) LINCS WARNING