[gmx-users] REMD simulation

Hi all, and thanks Mark, Chris and Xavier for your comments. I finally managed to run the REMD simulation but i can not restart the simulation or continue the simulation after it finished. I tried with a test system and run two replicas for just 20 ps. After it finished correctly i extended

Re: [gmx-users] REMD simulation

That looks very strange. Please file an issue at redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to me. Mark On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez ke...@mpi-muelheim.mpg.de wrote: Hi all, and thanks Mark, Chris and Xavier for your comments. I finally

Re: [gmx-users] REMD simulation

Virtual sites also have a hidden benefit - not only can you take a longer time step, but the width of the distribution of PE is relatively wider, so you can have higher exchange probability for the same temperatures. Mark On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale

[gmx-users] REMD simulation

Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried

Re: [gmx-users] REMD simulation

Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the

[gmx-users] REMD simulation

Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There

[gmx-users] REMD simulation of peptide-membrane system

Dear all, I'd like to do folding simulations of a short peptide on membrane surface using REMD using atomistic FF. But the problem is that membrane will disrupt at high temperatures. To maintain the membrane structure, I am thinking the following two methods: (1) To use different coupling

Re: [gmx-users] REMD simulation of peptide-membrane system

On 03/03/11, Jianguo Li ljg...@yahoo.com.sg wrote: !-- DIV {margin:0px;} -- Dear all, I'd like to do folding simulations of a short peptide on membrane surface using REMD using atomistic FF. But the problem is that membrane will disrupt at high temperatures. To maintain the