<div>Dear users, </div>
<div>I am trying to simulate a non protein molecule and have included the necessary parameters in the ff*.rtp file. I first encountered an error in the grompp step, so i modified my .mdp files such that the rlist, rvdw and rcoulomb values are set to 0.5. Now, while carrying out the mdrun for the position restraint step, I am getting a segmentation fault and a LINCS warning for the dihedrals that exceed 30. I do not know how to proceed and I'm using version 3.3.3 so the bug in the earlier version should have been fixed. I have also tried other suggestions in the forum with no effect. Here is my pr.mdp file<br>
<br><br>title = cpeptide position restraining<br>warnings = 10<br>cpp = /lib/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 10000 ; total 20.0 ps.<br>nstcomm = 1<br>nstxout = 10<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>
nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>fourierspacing = 0.12<br>pme_order = 4<br>ewald_rtol = 1e-5<br>rlist = 0.5<br>coulombtype = PME<br>
rcoulomb = 0.5<br>rvdw = 0.5<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tau_t = 0.1 0.1<br>tc-grps = Protein other<br>
ref_t = 300 300 <br>; Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br><br>and this is the error I am encountering.<br><br>Back Off! I just backed up md.log to ./#md.log.2#<br>Reading file NOR_pr.tpr, VERSION 3.3.3 (single precision)<br>
<br>Back Off! I just backed up ener.edr to ./#ener.edr.2#<br>starting mdrun 'Protein in water'<br>10000 steps, 20.0 ps.<br><br><br>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
max 361281.968750 (between atoms 2 and 7) rms 231973.328125<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 1 2 89.7 0.1530 43840.2148 0.1530<br>
1 5 89.8 0.1530 44279.3516 0.1530<br> 2 3 89.3 0.1530 51527.6133 0.1530<br> 2 7 89.1 0.1530 55276.2969 0.1530<br> 3 4 89.5 0.1530 22948.2949 0.1530<br>
3 6 88.5 0.1530 20192.1895 0.1530<br> 4 5 88.8 0.1530 8407.1387 0.1530<br> 4 7 89.3 0.1530 26344.8340 0.1530<br> 5 6 91.3 0.1530 33359.8477 0.1530<br>
6 7 88.6 0.1530 13846.0684 0.1530<br>Segmentation fault<br><br><br>I have been trying to solve this problem for quite some time now. It would be very helpful if you can suggest some way to work around this problem. <br>
regards<br>Rukmani Sridharan<br></div>