Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Hi Justin, I tried "unconstrained_start = yes". It did not work. I freeze CNT, CMT groups rather than constraints. To try from scratch, I deleted all the groups apart from CNT and CMT, then solvated the box with water. I ran a short simulation for 5000 steps, it runs fine. But when I tried to res

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: I usually use the final output file generated by GROMACS which contain the velocity. But, I dont preserve the velocity every timestep. CNT, CMT are constrained. I would want to make them move only in X direction, but I cannot make the simulation work even when th

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

> Can you post the relevant .mdp file(s)? Are you preserving velocity > information from the previous trajectory, or generating new velocities? Are > any of the species in your system constrained? > > -Justin > I usually use the final output file generated by GROMACS which contain the velocity.

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: Dear Justin, The initial configuration for this simulation is the configuration obtained from 10 ns of simulation. The only thing that is changed is that I now consider a nanotube as a single rigid body connected by bonds, so that I can make the nanotube move alo

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Dear Justin, The initial configuration for this simulation is the configuration obtained from 10 ns of simulation. The only thing that is changed is that I now consider a nanotube as a single rigid body connected by bonds, so that I can make the nanotube move along the x-direction as a whole. I d

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: Dear Mark, Some groups which were constrained in all 3 dimensions in one .mdp whereas in other .mdp that groups were not constrained in x-direction. But now I used same .mdp file and now even "nrdf" are same. Strangely (common atleast when doing this simulation),

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Dear Mark, Some groups which were constrained in all 3 dimensions in one .mdp whereas in other .mdp that groups were not constrained in x-direction. But now I used same .mdp file and now even "nrdf" are same. Strangely (common atleast when doing this simulation), the total energy and other thermo

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: Dear Mark, When I compare the .tpr files the following is the online line where its different "inputrec->grpopts.nrdf[0] (8.240200e+04 - 8.110200e+04)" IIRC "nrdf" is short for "number of degrees of freedom" which in turn suggests that the number of constraints has

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Dear Mark, When I compare the .tpr files the following is the online line where its different "inputrec->grpopts.nrdf[0] (8.240200e+04 - 8.110200e+04)" When I compare two energy files, "LJ-SR:FMN-CNTstep 0: -588.918, step 0: 2.06986e+18 LJ-SR:FMN-CMTstep 0: -558.573, st

Re: [gmx-users] weird mdrun...using gromacs 3.3.3

Naga Rajesh Tummala wrote: Dear All, Two simulations runs starting from same initial configuration results in very different energies in the first step. Both are identical simulations, nothing is changed. Did anybody encounter such problem before ? If yes, can you let me know what to do to fix t

[gmx-users] weird mdrun...using gromacs 3.3.3

Dear All, Two simulations runs starting from same initial configuration results in very different energies in the first step. Both are identical simulations, nothing is changed. Did anybody encounter such problem before ? If yes, can you let me know what to do to fix this problem. Below are the e