[gmx-users] pull code absolute reference artifacts

[Berk Hess]

Hi,

I have no clue why you would want to fix the peptide in the middle of the box.
But what you want seems to be more like com removal for the peptide only
with the comm options.
The pull code will do approximately what you want, but with pressure coupling
there is the problem that your peptide will stay fixed in space, while the rest
of the system has to scale around it.

In general there are problems with absolute reference pulling, because you just
fix the location of the pull group, whereas the rest of the system can freely move,
thus the net effect is zero, except for lots of nasty artifacts when you change
the pull position too fast.

Berk

> Date: Thu, 16 Apr 2009 10:27:04 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code absolute reference artifacts
> 
> Hello,
> 
> I have a question about the following grompp 4.0.4 warning:
> 
> "You are using an absolute reference for pulling, but the rest of the  
> system does not have an absolute reference. This will lead to  
> artifacts."
> 
> While I do realize that this is an excellent error message containing  
> lots of information, I am still unclear about how to proceed. Why does  
> my system not have an absolute reference? Is it because I have pbc and  
> center of mass motion removal? Exactly what types of artifacts are  
> expected? Is there a simple solution?
> 
> I am trying to hold my peptide in the center of a water box. I realize  
> that there is no "center" and everything in pbc, but I need to do it  
> nevertheless.
> 
> Here are my .mdp options:
> 
> pull                = umbrella
> pull_geometry       = distance
> pull_dim            = Y Y Y
> pull_ngroups        = 1
> ;pull_group0         =
> pull_group1         = peptide_A
> pull_k1             = 500
> pull_init1          = 0.00
> 
> nsteps              =  250000             ; REMOVE_FOR_EM
> tinit               =  49000              ; REMOVE_FOR_EM
> dt                  =  0.004              ; REMOVE_FOR_EM
> nstxout             =  250000             ; REMOVE_FOR_EM
> nstvout             =  250000             ; REMOVE_FOR_EM
> nstfout             =  250000             ; REMOVE_FOR_EM
> nstenergy           =  25000     ; REMOVE_FOR_EM
> nstxtcout           =  25000     ; REMOVE_FOR_EM
> nstlog              =  250000    ; REMOVE_FOR_EM
> gen_vel             =  no
> unconstrained-start =  yes
> 
> integrator          =  sd
> gen_seed            =  -1
> comm_mode           =  linear
> nstcomm             =  1
> comm_grps           =  System
> nstlist             =  5
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  PME
> rcoulomb            =  0.9
> fourierspacing      =  0.12
> pme_order           =  4
> vdwtype             =  cut-off
> rvdw_switch         =  0
> rvdw                =  1.4
> rlist               =  0.9
> DispCorr            =  EnerPres
> Pcoupl              =  Berendsen          ; REMOVE_FOR_EM
> pcoupltype          =  isotropic          ; REMOVE_FOR_EM
> compressibility     =  4.5e-5             ; REMOVE_FOR_EM
> ref_p               =  1.                 ; REMOVE_FOR_EM
> tau_p               =  4.0                ; REMOVE_FOR_EM
> tc_grps             =  System             ; REMOVE_FOR_EM
> tau_t               =  1.0                ; REMOVE_FOR_EM
> ld_seed             =  -1                 ; REMOVE_FOR_EM
> ref_t               =  300.               ; REMOVE_FOR_EM
> gen_temp            =  300.               ; REMOVE_FOR_EM
> constraints         =  all-bonds          ; REMOVE_FOR_EM
> constraint_algorithm=  lincs              ; REMOVE_FOR_EM
> lincs-iter          =  1                  ; REMOVE_FOR_EM
> lincs-order         =  6                  ; REMOVE_FOR_EM
> 
> 
> _______________________________________________
> 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/20090417/282e771a/attachment.html>