[gmx-users] How to fix protein went out water?

Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation?  Best regards, Batsaikhan  -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] How to fix protein went out water?

On 6/17/14, 7:56 AM, Batdorj Batsaikhan wrote: Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin

Re: [gmx-users] How to fix protein went out water?

Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan...@yahoo.com: Dear gmx_users, I am working on simulation of protein in water. 10 ns

Re: [gmx-users] How to fix protein went out water?

On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this with the editconf) There is no need to re-do anything. PBC means it is totally irrelevant whether the protein is conveniently

Re: [gmx-users] How to fix protein went out water?

Thank you Justin and Thales. Best regards, Batsaikhan On Tuesday, June 17, 2014 11:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 10:54 AM, Thales Kronenberger wrote: Hi Batsaikhan You should re-do the simulation, perfoming it within a box of water with PBC (you can do this