[gmx-users] Deletion of Lipids During InflateGro?

Dear Gromacs Users, I am working on building a lipid bilayer for my protein structure but I am having difficulty using the InflateGRO script. I am using a POPC bilayer and used the genconf command to extend the length of the bilayer so I would be able to go from having 128 to 256 lipids. The

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

Sorry, didn't notice the cpt files weren't yet generated. Justin is always right about everything. Alex On 12/29/2016 1:58 PM, Zhang, Cheng wrote: Hi Justin, Thank you very much. It worked as you said [] Yes, I was only using 10 min in the beginning, so no cpt file could be generated.

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

Hi Justin, Thank you very much. It worked as you said [] Yes, I was only using 10 min in the beginning, so no cpt file could be generated. Yours sincerely Cheng From: Zhang, Cheng Sent: 29 December 2016 19:02:47 To:

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

On 12/29/16 2:02 PM, Zhang, Cheng wrote: Hi Alex, Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, I still ONLY got the four files WITHOUT cpt file. ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log I know the link

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

Hi Alex, Thank you. I tested "mdrun_mpi -deffnm md_0_1 -cpi state.cpt -append". However, I still ONLY got the four files WITHOUT cpt file. ) md_0_1.trr ) md_0_1.xtc ) md_0_1.edr ) md_0_1.log I know the link http://www.gromacs.org/Documentation/How-tos/Extending_Simulations, but is it for

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

add "-cpi state.cpt -append " into your mdrun command and submit it. This is useful: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Alex On Dec 29, 2016 11:24 AM, "Zhang, Cheng" wrote: > Dear Gromacs, > I would like to extend my simulation. > > 200 ns

[gmx-users] How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs, I would like to extend my simulation. 200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr". Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr". Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job finishes. The