[gmx-users] Re: pulling

[Thomas Schlesier]

Could it also be possible that 'pull = distance' makes problems because
it pulls both groups and here one group is frozen? Only an idea, i have
never tried to pull a frozen molecule.
Thomas


> ------------------------------
> 
> Message: 5
> Date: Fri, 31 Jul 2009 12:38:19 +0200
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] pulling
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W5604F1D24936CF27D18DFE8E100 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Ah, then you could have a pbc problem for determining the COM of the slab,
> since you slab is thicker than half the box.
> You have to set pull_pbcatom0 to an atom in the middle of the slab.
> 
> pull_init1 doesn't change.
> The only thing the geometry change affects is the direction you pull in.
> With distance you could be unlucky that it takes the distance
> in the opposite direction.
> 
> Berk
> 
>> Date: Fri, 31 Jul 2009 12:32:13 +0200
>> From: alexander.herz at mytum.de
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] pulling
>>
>> Thx for the quick reply!
>>
>> I use 4.0.5, pbc z=yes
>> Box height = 17.5nm
>> gld slab is from z=0 to z= 9.5;
>> So distance=5.5 should give 1.0nm above surface right?
>>
>> What do I have to put for pull_init1 if i use direction??
>>
>> Thx,
>> Alex
>>
>> Berk Hess schrieb:
>>> Hi,
>>>
>>> I hope you are using 4.0.5, I fixed several bug in the pull code for
>>> older 4.0 versions.
>>>
>>> The problems you are seing could be due to  pbc.
>>> Do you have pbc in Z, and what is the height of your box?
>>>
>>> A safer setup is:
>>> pull_geometry = direction
>>> pull_vec1 = 0 0 1
>>> But they should give the same answers if you do not have pbc issues.
>>>
>>> Berk
>>>
>>>> Date: Fri, 31 Jul 2009 12:13:07 +0200
>>>> From: alexander.herz at mytum.de
>>>> To: gmx-users at gromacs.org
>>>> Subject: [gmx-users] pulling
>>>>
>>>> Hey,
>>>>
>>>> I appear to have serious trouble understanding how to set up the pulling
>>>> properly.
>>>>
>>>> I have many configurations of a protein partially adsorbed to a froozen
>>>> surface (the configs differ
>>>> in the amount of the protein that has been desorbed).
>>>> Now I want the pulling to keep the distance of the desorbed end of the
>>>> protein to the surface using the harmonic pot.
>>>> Now the documentation is not very clear how this all works so I ran
>>>> several experiments to figure it out but I failed.
>>>> I use the following options:
>>>>
>>>> ;PULLING
>>>> pull = umbrella
>>>> pull_geometry = distance
>>>> pull_dim = N N Y
>>>> pull_nstxout = 1000
>>>> pull_nstfout = 1000
>>>> pull_ngroups = 1
>>>> pull_group0 = GLD
>>>> pull_group1 = ASN
>>>> pull_vec1 = 0.0 0.0 0.0
>>>> pull_init1 = 5.27778
>>>> pull_rate1 = 0.0
>>>> pull_k1 = 100
>>>>
>>>>
>>>> where gld is the surface and asn is the end residue of the protein and
>>>> pull_init1 is set to the desired COM distance of the two
>>>> groups (gld is froozen). I use the same settings for all runs, only
>>>> changing pull_init1 to get the desired distance.
>>>> Now for some reason using this setup either pulls the ASN end of the
>>>> protein completely onto the surface or very far away from it depending
>>>> on the value I use for pull_init1.
>>>> So the distance between what and what shall I put for pull_init1? What
>>>> else is wrong?
>>>>
>>>> Thx,
>>>> Alex
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.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! MSN Messenger
>>> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.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://lists.gromacs.org/pipermail/gmx-users/attachments/20090731/22c5d4e2/attachment.html
> 
> ------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 
> End of gmx-users Digest, Vol 63, Issue 161
> ******************************************