[gmx-users] Re: gmx-users Digest, Vol 47, Issue 12
Grace Li
fullofgrace88 at gmail.com
Thu Mar 6 14:14:29 CET 2008
Here is a few more replies relating to your question.
On Thu, Mar 6, 2008 at 12:09 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Problem with using distance restraints (disre) with PBC
> (TJ Piggot)
> 2. Re: Problem with using distance restraints (disre) with PBC
> (Mitchell Stanton-Cook)
> 3. lateral diffusion coefficient of bilayer (LeeHwan-kyu)
> 4. Re: lateral diffusion coefficient of bilayer (Justin A. Lemkul)
> 5. Re: Problems with OPLS topology files (Mark Abraham)
> 6. Checking the Progress of Energy minimization (s lal badshah)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 06 Mar 2008 02:03:12 +0000
> From: TJ Piggot <t.piggot at bristol.ac.uk>
> Subject: Re: [gmx-users] Problem with using distance restraints
> (disre) with PBC
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <3F4603EBE23F583CBC03F0AB at localhost.localdomain>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> I agree with increasing the size of the box (if seeing inconsistent shifts,
> as i should have mentioned in my previous post) and in this case it is
> practical to do as the system is quite small. However (just for future
> reference) if the problem were in a much larger system (as it is in my
> case) then it may be more suitable to modify the source code to avoid
> increasing the size of the system simulated.
>
> Tom
>
> --On Thursday, March 06, 2008 11:52:01 +1000 Mitchell Stanton-Cook
> <s4026869 at student.uq.edu.au> wrote:
>
> > I have had a similar problem with orientation restraints.
> >
> > Are the residues far is space? Are you getting inconsistent shifts? If so
> > -
> >
> > If so re-define your box size so that the shortest box vector is greater
> > than the distance restraint residue + some tolerance.
> >
> > I also noticed -
> >
> > [ distance_restraints ]
> > ;ai aj type index type low up1 up2 fac
> > 9 413 1 0 1 8.18 8.18 10.0
> > 1.0
> >
> > Have you defined the low up and up2 in the correct units?
> >
> > Cheers
> >
> > Mitch
> >
> > TJ Piggot wrote:
> >> Hi,
> >>
> >> Firstly I would strongly reiterate what Mark said. I would make sure
> >> the distance restraints are causing your problem. Again as Mark said
> >> make sure you can simulate your system without the distance
> >> restraints, and then I would try to simulate the system with distance
> >> restraints and with a much larger box of water surrounding your
> >> peptide. Here you should also be able to overcome the problem (if it
> >> is this problem) with a large enough distance between periodic images.
> >>
> >> If you can then confirm what you have suspected to be the problem you
> >> will need to modify the source code slightly. If you search the list
> >> (searching for "inconsistent shifts using multiple bonds type 6") you
> >> can see the changes you need to make, as suggested by Berk Hess to me
> >> when i had this problem with bond type 6.
> >>
> >>
> >> Hope this helps
> >>
> >> Cheers
> >>
> >> Tom
> >>
> >> --On Wednesday, March 05, 2008 17:16:23 -0500 Grace Li
> >> <fullofgrace88 at gmail.com> wrote:
> >>
> >>> Hello,
> >>> I am having some trouble using distance restraints. My goal is to
> >>> apply a
> >>> harmonic potential to the distance between two atoms in a short peptide
> >>> (35 residues). Doing simulations in vacuo, both of the following
> >>> techniques worked to restrain the distance. Also, both techniques worked
> >>> for simulations in water without periodic boundary conditions. As soon
> >>> as I include pbc = xyz in my .mdp file and use PME for the
> >>> electrostatics, my simulation crashes (producing step0.pdb and
> >>> step-1.pdb). I am assuming this is because GROMACS is using the distance
> >>> to the image of the other atom, not the actual distance in the box? Is
> >>> there any way of getting around PBC for distance restraints?
> >>>
> >>> Specifically, I have used the following:
> >>>
> >>> 1. I have tried using bonds type 6 in my topology:
> >>> [ bonds ]
> >>> ; ai aj funct c0 c1 c2 c3
> >>> 9 413 6 8.18 421.54
> >>>
> >>> 2. When using distance restraints, I added the following lines to my
> >>> topology file:
> >>> [ distance_restraints ]
> >>> ;ai aj type index type low up1 up2 fac
> >>> 9 413 1 0 1 8.18 8.18 10.0
> >>> 1.0
> >>>
> >>> In the case of using [ distance_restraints ] in the topology file, I
> >>> have
> >>> added the following lines to my .mdp file:
> >>> disre = simple
> >>> disre_fc = 421.54
> >>> disre_weighting = equal
> >>> disre_tau = 0
> >>> (and various other values of the force constant, disre_fc, but in all
> >>> cases the run crashes).
> >>>
> >>> Thanks for any suggestions!
> >>> _______________________________________________
> >>> 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
> >>
> >>
> >>
> >> ----------------------
> >> TJ Piggot
> >> t.piggot at bristol.ac.uk
> >> University of Bristol, UK.
> >>
> >> _______________________________________________
> >> 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
> >>
> >
> > _______________________________________________
> > 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
>
>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 06 Mar 2008 12:50:18 +1000
> From: Mitchell Stanton-Cook <s4026869 at student.uq.edu.au>
> Subject: Re: [gmx-users] Problem with using distance restraints
> (disre) with PBC
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47CF5BEA.90002 at student.uq.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Tom,
>
> Have you modified the src? As far as I know this has not been done in
> 331 or 332. I'm unsure of 333. I would be interested in the patch. As
> far as I know the problem is due to the the distance/orientation
> restraints being placed in the bonded graph. There was a bit of chatter
> on the developers list in 2007 about this but I haven't heard much else.
>
> For my system I was using a truncated dodecahedron box. The box vector
> 1/2d was my biggest problem. I simply changed to a triclinic box without
> too much cost. However I think I could grab an extra 300ps/day if I had
> an actual fix.
>
>
> Cheers
>
> Mitch
>
> TJ Piggot wrote:
> > I agree with increasing the size of the box (if seeing inconsistent
> > shifts, as i should have mentioned in my previous post) and in this
> > case it is practical to do as the system is quite small. However (just
> > for future reference) if the problem were in a much larger system (as
> > it is in my case) then it may be more suitable to modify the source
> > code to avoid increasing the size of the system simulated.
> >
> > Tom
> >
> > --On Thursday, March 06, 2008 11:52:01 +1000 Mitchell Stanton-Cook
> > <s4026869 at student.uq.edu.au> wrote:
> >
> >> I have had a similar problem with orientation restraints.
> >>
> >> Are the residues far is space? Are you getting inconsistent shifts?
> >> If so
> >> -
> >>
> >> If so re-define your box size so that the shortest box vector is greater
> >> than the distance restraint residue + some tolerance.
> >>
> >> I also noticed -
> >>
> >> [ distance_restraints ]
> >> ;ai aj type index type low up1 up2 fac
> >> 9 413 1 0 1 8.18 8.18 10.0
> >> 1.0
> >>
> >> Have you defined the low up and up2 in the correct units?
> >>
> >> Cheers
> >>
> >> Mitch
> >>
> >> TJ Piggot wrote:
> >>> Hi,
> >>>
> >>> Firstly I would strongly reiterate what Mark said. I would make sure
> >>> the distance restraints are causing your problem. Again as Mark said
> >>> make sure you can simulate your system without the distance
> >>> restraints, and then I would try to simulate the system with distance
> >>> restraints and with a much larger box of water surrounding your
> >>> peptide. Here you should also be able to overcome the problem (if it
> >>> is this problem) with a large enough distance between periodic images.
> >>>
> >>> If you can then confirm what you have suspected to be the problem you
> >>> will need to modify the source code slightly. If you search the list
> >>> (searching for "inconsistent shifts using multiple bonds type 6") you
> >>> can see the changes you need to make, as suggested by Berk Hess to me
> >>> when i had this problem with bond type 6.
> >>>
> >>>
> >>> Hope this helps
> >>>
> >>> Cheers
> >>>
> >>> Tom
> >>>
> >>> --On Wednesday, March 05, 2008 17:16:23 -0500 Grace Li
> >>> <fullofgrace88 at gmail.com> wrote:
> >>>
> >>>> Hello,
> >>>> I am having some trouble using distance restraints. My goal is to
> >>>> apply a
> >>>> harmonic potential to the distance between two atoms in a short
> >>>> peptide
> >>>> (35 residues). Doing simulations in vacuo, both of the following
> >>>> techniques worked to restrain the distance. Also, both techniques
> >>>> worked
> >>>> for simulations in water without periodic boundary conditions. As soon
> >>>> as I include pbc = xyz in my .mdp file and use PME for the
> >>>> electrostatics, my simulation crashes (producing step0.pdb and
> >>>> step-1.pdb). I am assuming this is because GROMACS is using the
> >>>> distance
> >>>> to the image of the other atom, not the actual distance in the box? Is
> >>>> there any way of getting around PBC for distance restraints?
> >>>>
> >>>> Specifically, I have used the following:
> >>>>
> >>>> 1. I have tried using bonds type 6 in my topology:
> >>>> [ bonds ]
> >>>> ; ai aj funct c0 c1 c2 c3
> >>>> 9 413 6 8.18 421.54
> >>>>
> >>>> 2. When using distance restraints, I added the following lines to my
> >>>> topology file:
> >>>> [ distance_restraints ]
> >>>> ;ai aj type index type low up1 up2 fac
> >>>> 9 413 1 0 1 8.18 8.18 10.0
> >>>> 1.0
> >>>>
> >>>> In the case of using [ distance_restraints ] in the topology file, I
> >>>> have
> >>>> added the following lines to my .mdp file:
> >>>> disre = simple
> >>>> disre_fc = 421.54
> >>>> disre_weighting = equal
> >>>> disre_tau = 0
> >>>> (and various other values of the force constant, disre_fc, but in all
> >>>> cases the run crashes).
> >>>>
> >>>> Thanks for any suggestions!
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>>
> >>>
> >>> ----------------------
> >>> TJ Piggot
> >>> t.piggot at bristol.ac.uk
> >>> University of Bristol, UK.
> >>>
> >>> _______________________________________________
> >>> 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
> >>>
> >>
> >> _______________________________________________
> >> 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
> >
> >
> >
> > ----------------------
> > TJ Piggot
> > t.piggot at bristol.ac.uk
> > University of Bristol, UK.
> >
> > _______________________________________________
> > 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
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Mar 2008 22:41:35 -0500
> From: LeeHwan-kyu <hklee910 at hotmail.com>
> Subject: [gmx-users] lateral diffusion coefficient of bilayer
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY105-W51E37A31B14675D1316FD998120 at phx.gbl>
> Content-Type: text/plain; charset="ks_c_5601-1987"
>
>
> Dear gmx-users,
>
> I have some questions about calculation of lateral diffusion coefficient for bilayer. I've searched this forum, but I still have problems.
>
> 1) I'm trying to get lateral diffusion coefficient of the lipid bilayer , and I typed "g_msd -f ***.xtc -s ***.tpr -o msd.xvg -b 30000 -e 40000 -beginfit 1000 -endfit 7000 -lateral z". I got too high D value (which is shown as D[ xxx] 0.5412 (+/- 0.0021) 1e-5 cm^2/s. I calculated it for each monolayer, and also for bilayer, but had similar values. This big value comes from the size effect ? Is there anyway to get a reasonable lateral D?
>
> 2) When I ran the bilayer simulation, did I have to remove center of mass for each monolayer? My input script is jut like below. Do I need to write commends for center of mass removal for each monolayer, and run simulations again?
> -------
> nstcomm = 1
> comm-grps =
> -------
>
> Thank you for your help in advance.
>
> best,
> Hwankyu.
>
>
> _________________________________________________________________
> MSN ¸Þ½ÅÀúÀÇ Â÷¼¼´ë ¹öÀü, Windows Live Messenger!
> http://windowslive.msn.co.kr/wlm/messenger/
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> ------------------------------
>
> Message: 4
> Date: Wed, 5 Mar 2008 23:04:22 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] lateral diffusion coefficient of bilayer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1204776262.47cf6d46cf02e at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
>
> Did you follow the thread I started here:
>
> http://www.gromacs.org/pipermail/gmx-users/2008-January/031797.html
>
> I got some great information when I was getting some strange values for D. What
> group are you using to calculate D? The suggestion that David gave me about
> using P atoms only for the calculation led me to much more reasonable results.
>
> -Justin
>
> Quoting LeeHwan-kyu <hklee910 at hotmail.com>:
>
> >
> > Dear gmx-users,
> >
> > I have some questions about calculation of lateral diffusion coefficient for
> > bilayer. I've searched this forum, but I still have problems.
> >
> > 1) I'm trying to get lateral diffusion coefficient of the lipid bilayer , and
> > I typed "g_msd -f ***.xtc -s ***.tpr -o msd.xvg -b 30000 -e 40000 -beginfit
> > 1000 -endfit 7000 -lateral z". I got too high D value (which is shown as D[
> > xxx] 0.5412 (+/- 0.0021) 1e-5 cm^2/s. I calculated it for each monolayer,
> > and also for bilayer, but had similar values. This big value comes from the
> > size effect ? Is there anyway to get a reasonable lateral D?
> >
> > 2) When I ran the bilayer simulation, did I have to remove center of mass for
> > each monolayer? My input script is jut like below. Do I need to write
> > commends for center of mass removal for each monolayer, and run simulations
> > again?
> > -------
> > nstcomm = 1
> > comm-grps =
> > -------
> >
> > Thank you for your help in advance.
> >
> > best,
> > Hwankyu.
> >
> >
> > _________________________________________________________________
> > MSN ¸Þ½ÅÀúÀÇ Â÷¼¼´ë ¹öÀü, Windows Live Messenger!
> > http://windowslive.msn.co.kr/wlm/messenger/
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 06 Mar 2008 15:06:20 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Problems with OPLS topology files
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47CF6DBC.9080507 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Goran Krilov wrote:
> > Thanks!
> > I am enclosing the piece of the topology file (2607 is the first line
> > after the
> > [dihedrals] heading:
> >
> > 342 97 98 105 3 0.62760 1.88280 0.00000 -2.51040
> > 0.0000 0.0000
> > 342 97 323 324 3 0.00000 0.00000 0.00000 0.00000
> > 0.0000 0.0000
> > 342 97 323 327 3 0.00000 0.00000 0.00000 0.00000
> > 0.0000 0.0000
> >
> > [ dihedrals ]
> >
> > ; ai aj ak al funct c0 c1 c2 c3
> > c4 c5
> > 2 5 1 25 1 8.36800 0.00000 -8.36800 0.00000
> > 0.0000 0.0000
>
> Look at Table 5.4... dihedral function type 1 doesn't take 6 parameters.
> Because it is actually expecting 3, gromacs infers that because 6 =
> 2*3 that you're trying to do a free-energy perturbation calculation.
> This explains the error message.
>
> Mark
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 6 Mar 2008 05:09:06 +0000 (GMT)
> From: s lal badshah <shahbiochemist at yahoo.com>
> Subject: [gmx-users] Checking the Progress of Energy minimization
> To: gromacs <gmx-users at gromacs.org>
> Message-ID: <299026.97381.qm at web53005.mail.re2.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
> I am doing Energy minimization of a protein.The valus are fluctuating butI don't know in how much time it will be completed and what are the signs that show that it is running?
>
> top - 09:54:08 up 22:52, 2 users, load average: 0.07, 0.17, 0.16
> Tasks: 111 total, 1 running, 109 sleeping, 1 stopped, 0 zombie
> Cpu(s): 6.7%us, 2.3%sy, 0.0%ni, 89.6%id, 0.6%wa, 0.8%hi, 0.0%si, 0.0%st
> Mem: 1025804k total, 980436k used, 45368k free, 201956k buffers
> Swap: 2104444k total, 0k used, 2104444k free, 454128k cached
>
>
> Please guide me.
> Regrads,
> Lalbadshah
>
>
> SYED LAL BADSHAH
> M.Phil Scholar
> NCE in Physical Chemistry,
> University of Peshawar.
> NWFP,Pakistan.
> Cell # 03349060632.
> Send instant messages to your online friends http://uk.messenger.yahoo.com
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>
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