Thank you Justin,<br>I have tried to just solvate the peptide in water box using genbox command and spc216 water<br>Then I have used the Energy Min mdp file form your tutorial (I have been folowing your tutorial for couple of days, the difference is that I want to put my segment on top of the membrane between the head groups of phospholipids). The DMPC box is stable, but I have trouble with 14aa peptide. It seems that is is unstable, I have made NH2 and COOO termini, maybe this is the problem?<br>
<br>The results of EM for peptide in water:<br><br>Step= 786, Dmax= 6.3e-03 nm, Epot= -1.37798e+06 Fmax= 7.60491e+02, atom= 67<br><br>writing lowest energy coordinates.<br><br>Steepest Descents converged to Fmax < 1000 in 787 steps<br>
Potential Energy = -1.3779814e+06<br>Maximum force = 7.6049121e+02 on atom 67<br>Norm of force = 1.8584177e+01<br><br>Then I run mdrun using mdp file that we use usually in our lab, and system crashed with LINCS warnings after 75 steps.<br>
<br>But when I use the mdp file that is in EM section of your tutorial and change integrator = md. The peptide in water system is running without any warnings up till step 300.<br><br>step 300, Warning: 1-4 interaction between 54 and 59 at distance 2.342 which is larger than the 1-4 table size 2.200 nm<br>
<br>What settings would you recommend for MD runs in mdp files?<br><br>Could you explain from your tutorial:<br><br>How to Reduce the charges on the H atoms (all the way to zero, if necessary) <font color="red">Restore the charges before continuing<br>
<br></font>And how Add <font face="courier" size="-1">[ exclusions ]</font> within the topology between H and phosphate O atoms <font color="red">Remove the exclusions before continuing</font><br><br>Thanks<br><br><br>