Hello fellow GMX users,<br><br>I've been digging in the archives and haven't yet found a good response to this question, so I thought I'd ask again, since I see from a post just last month others are still interested in this subject as well. Is it possible in Gromacs to periodically update/change the charges on a given molecule or residue during the course of a simulation?<br>
<br>What I am envisioning is having a production simulation running, and then every "x" amount of time, the current checkpoint file gets read and processed by an external routine that calculates charges on the residue or molecule of interest, which are then fed back into Gromacs to continue the run. Is it possible to execute an external program from within a Gromacs simulation? I know this functionality must be in there somewhere, since Gromacs can communicate with external QM software, but I'm not sure if a charge modification scheme could make use of the same built-in I/O methods.<br>
<br>Is such a scheme possible? I realize an alternative method would be to stop the run, do some calculation to recalculate the charges, and then perhaps use some simple code to modify the .top file directly, and finally grompp out a new tpr file and continue the run. Lather, rinse, repeat. I'm guessing this could be rather slow because of needing to call grompp over and over and the need to continually restart the simulation. <br>
<br>For what it's worth, my interest lies mainly in excited state chromophores and I'd be using modified ZINDO code to calculate charges every x number of steps. This calculation is *very* fast, even for large chromophores, therefore my focus on other performance bottlenecks.<br>
<br>I would be extremely grateful for any feedback on this subject, particularly from anyone who has done a similar thing successfully and cares to share any tips or code.<br clear="all"><br>-- <br>----------<br>J. Nathan Scott, Ph.D.<br>
Postdoctoral Fellow<br>Department of Chemistry and Biochemistry<br>Montana State University<br>