Re: [gmx-users] Pull code methods?

Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete

Re: [gmx-users] Pull code methods?

Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to

[gmx-users] Pull code methods?

Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling

Re: [gmx-users] Pull code with shuffle/sort options

Thank you Chris for providing recognition of this issue. -Steve Chris Neale wrote: I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the

[gmx-users] Pull code with shuffle/sort options

I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the dynamics of the molecule of interest appears to be unaffected by the pulling potential.

[gmx-users] pull code, constraint force

Hi, I am trying to calculate free energy and diffusivity of a guest molecule at a given height from lipid bilayer. I am using pull code with runtype=constraint, reftype=com, pulldim=N N Y in version 3.3.1 compiled in double precision. The ensemble is NPT (Nose-Hoover/ Parrinello-Rahman). To save

[gmx-users] pull code questions

Dear all, I had a couple quick questions on the pull code, as I couldn't quite figure this out from the documentation. In particular, I'm interested in the part that does umbrella sampling: 1) If an alternative reference structure is provided to grompp using the -r option (as one would do for

[gmx-users] pull code bug?

Dear all, sorry for the long message. I am simulating the hydrophobic interaction between two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent withall-bonds constraints (LINCS) by GROMACS 3.3 downloaded from GROMACS web-site. In order to allow them to interactI

[gmx-users] pull code question

Dear GMX users, I am simulating the hydrophobic interaction between two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent withall-bonds constraints (LINCS). In order to allow them to interact -for the first time-I am using pull code. My pull.ppa is as follows

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