[gmx-users] pull code absolute reference artifacts

[chris.neale at utoronto.ca]

Thanks for the explanation Berk,

I am simply trying to do some tests to ensure that the pull code and  
free energy code are working properly in combination. For this I tried  
to simplify my 'problem' and apply double-decoupling to a solute in a  
box of water under 2 conditions: 1) no pull code, and 2) pull code  
with an absolute reference to pin the decoupled molecule in place  
harmonically. Since the water box is isotropic, I should get the same  
overall free energy for decoupling (which I do in spite of the warning  
message, perhaps because I don't change the reference position over  
time).

Thanks again,
Chris.

-- original message --

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://www.gromacs.org/pipermail/gmx-users/attachments/20090417/282e771a/attachment.html