[gmx-users] extend phosphorylated simulation 43A1p

Mehreen Jan mehreen_jan1990 at yahoo.com
Fri May 6 12:34:40 CEST 2016

respected sir!
version 5.0.7
forcefield 43a1p
Question 1
i run  phosphorylated simulation 10ns result are good known i want to extend my simulation to 20ns the problem is at 11ns i generate PDB i am shocked to see that my TPO and SEP is no more in the pdb. structure is breakdown :( i have no idea what happen to my pdb :( :(

command to extend:

convert-tpr -s  md_0_1.tpr -extend 1000 -o next1.tpr

mdrun -s next1.tpr -cpi md_0_1.cpt

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