Dear Users, I am resending this mail, as I am still stuck with the error. Now I have upgraded my Gromacs from version-4.5.5. to version-5.0.2, I am able to run the simulation using Gromacs-5.0.2 for sytems with 1-octanol as solvent, whereas the system with water as solvent is still giving errors with LINCS warnings. I assume if the runs are going fine with water system then my topology and MDP (adapted from tutorial) files are in place, Please correct me if this is a wrong assumption. It will be really helpfull if anybody can help me in understanding the system behaviour or possible reasons for the error.
regards, Vivek ---------- Forwarded message ---------- From: vivek sharma <[email protected]> Date: 10 October 2014 09:01 Subject: Running free energy tutorial for ionic molecules To: Discussion list for GROMACS users <[email protected]> Hi users and experts, I am trying to run a free energy tutorial by Dr Lemkul provided at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/ My system is an ionic pyridinium molecule unlike the methane molecvule used in the tutorial, following are the steps I am following for my runs: 1. I downloaded the molecule structure and topology from ATB site: http://compbio.biosci.uq.edu.au/atb/index.py?tab=existing_tab&nocache=153 2. I set up the system using octanol water box. 3. I am using the MDP parameters as suggested in the advanced application section: decoupling vdw and coulombic interaction step by step. 4. WHile running the simulation it goes fine till npt equilibration step, but it fails during the production run with the LINCS warnings, like some angles are rotating more than 30 degree. I am unable to figure out if I can apply this protocol on ionic molecules or I am doing something wrong in setting up the system. Can somebody help me in understanding the possible reason for error? It will be really helpful to get more insights into this type of simulation. Thanks and regards, Vivek -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
