Re: [gmx-users] Pull code with runtype start

I searched the on line document for runtype and got nothing. But in the Manual in chapter 6 there is an overveiw of the pull code options and one of the options listed is the "starting structures" and it says the keyword for runtype to use for this is "start". On 10/19/07 6:55 PM, "Mark Abraham

Re: [gmx-users] Pull code with runtype start

dtmirij wrote: Hello everyone, I just want to clarify if the runtype "start" option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. Did you try searching the manual for "runtype"? Mark ___ gmx-users mai

[gmx-users] Pull code with runtype start

Hello everyone, I just want to clarify if the runtype "start" option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. If I have runtype = start in my pull.ppa file then gromacs gives me an error:

Re: [gmx-users] Pull code methods?

I'm no umbrella user, but as far as I know, you have to set different parameters, according to the manual. These may be similar to the AFM parameters, but still, in the config file, they are separated. Sure, you don't define a pull rate for Umbrella, because you build, as you said, discrete syst

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 sim

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 o

[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 (contraint_rat

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 dy

[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 with shuffle/sort options

Dear all, 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

[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 po

[gmx-users] Pull code with angle constraints

Dear gromacs gurus I wonder to know if there is some straightforward way to implement angle, dihedral and possibly other constraints to the pull code, beside distance constraints. Any idea would help. Sincerely Vojtech Spiwok --- Ing. Vojtech Spiwok, PhD. De

[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 with all-bonds constraints (LINCS) by GROMACS 3.3 downloaded from GROMACS web-site.   In order to allow them to interact I

[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 with all-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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