[gmx-users] how to set pull code in gmx 4

[Berk Hess]

Hi,

Have you looked at the mdp options help in the pdf or html manual?
The html manual is not online yet for 4.0, but you can find it in your Gromacs
directory at: share/html/online/mdp_opt.html

If you use pull_geometry=distance you need to set the reference distance,
which would be (assuming you want 1 nm):
pull_init1 = 1

Berk


> Date: Sat, 18 Oct 2008 22:45:38 +0800
> From: liyang1980_0_0 at 163.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] how to set pull code in gmx 4
> 
> Dear all
> 
> I cannot understand the explanations about settings of pull code in the
> gmx 4.
> 
> Take a example, there are two particles in the system, and I want to
> reproduce the LJ potential using "umbrella sampling".
> The settings in gmx 3.3.3 is following:
> =====================
> ..........
> runtype = umbrella
> ngroups = 1
> group_1 = Arg2
> reference_group = Arg1
> ......
> pulldim = N N Y
> K1 = 700
> POS1 = 0 0 1
> ======================
> 
> But I don't know how to set it in gmx 4
> Following is the settings in gmx 4:
> ======================
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant_force
> pull = umbrella ; ---> "runtype" in gmx 3.3.3
> ; Pull geometry: distance, direction, cylinder or position
> pull_geometry = distance
> ; Select components for the pull vector. default: Y Y Y
> pull_dim = N N Y ; ---> "pulldim" in gmx 3.3.3
> ; Cylinder radius for dynamic reaction force groups (nm)
> pull_r1 = 1
> ; Switch from r1 to r0 in case of dynamic reaction force
> pull_r0 = 1.5
> pull_constr_tol = 1e-06
> pull_start = no
> pull_nstxout = 10
> pull_nstfout = 1
> ; Number of pull groups
> pull_ngroups = 1 ; ---> "ngroups" in gmx 3.3.3
> ; Group name, weight (default all 1), vector, init, rate (nm/ps),
> kJ/(mol*nm^2)
> pull_group0 = Arg2 ; ---> "reference_group" in gmx 3.3.3
> pull_weights0 =
> pull_pbcatom0 = 0
> pull_group1 = Arg1 ; ---> "group1" in gmx 3.3.3
> pull_weights1 =
> pull_pbcatom1 = 0
> pull_vec1 = 0.0 0.0 0.0
> pull_init1 = 0.0
> pull_rate1 = 0
> pull_k1 = 700 ; ---> "k1" in gmx 3.3.3
> pull_kB1 = 0
> ======================
> if right, which parameter corresponds with "pos1" in gmx3.3.3?
> 
> I must apologize in advance if I miss some details in the manual.
> 
> Thank you very much
> 
> Li Yang
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081020/926b4d6e/attachment.html>