[gmx-users] Re: gmx-users Digest, Vol 74, Issue 13
Ozge Engin
ozge.engin at gmail.com
Tue Jun 1 22:51:58 CEST 2010
Hi Xavier,
Ok, it would be better to talk with the average values together with the
corresponding error bars. For the system having smaller number of water
molecules the minimum of the PMF was around -4.31+-0.97 kJ/mol, and for the
other system it was around -1.75+-1.05 kJ/mol. Therefore, the difference is
significant.
Regards
On Tue, Jun 1, 2010 at 11:30 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: number of water molecules affects the PMF (XAvier Periole)
> 2. Re: Fatal error: Atom O in residue CO 1 not found in rtp
> entry with 3 atoms while sorting atoms (Nilesh Dhumal)
> 3. Re: Fatal error: Atom O in residue CO 1 not found in rtp
> entry with 3 atoms while sorting atoms (Justin A. Lemkul)
> 4. Re: Fatal error: Atom O in residue CO 1 not found in rtp
> entry with 3 atoms while sorting atoms (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 1 Jun 2010 21:41:42 +0200
> From: XAvier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-users] number of water molecules affects the PMF
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <92B14805-6ABD-4D17-AF3D-E6C88393DD7D at rug.nl>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote:
>
> > Hi all,
> >
> > I am trying to calculate the potential of mean force between the two
> > hydrophobic dipeptides (phenylalanine) in bulk water via constraint
> > pulling simulations. First, I calculated the mean force at each of
> > the constraint points, and then I integrated the mean force curve to
> > get the PMF.
> >
> > In order to test how big the effect of the number of water molecules
> > on the calculated PMF I performed two sets of simulations which
> > differed from each other in terms of only the number of water
> > molecules. I used 9000 water molecules in one set, and 7000 in the
> > other. The overall PMF for the latter was steeper than the former,
> > as I expected before. However, the minimum point for the former was
> > around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think
> > that the difference should not be that much since there is not a big
> > difference between the number of water molecules between the two sets.
> Could it be that the difference is within the error ? What happens if
> you
> cut your data of each simulation in two pieces? In other words are you
> converged?
> >
> > I searched the internet to find a study regarding the concentration
> > dependency of the PMF.
> >
> > Is this reasonable? Any suggestions?
> >
> > Regards
> >
> > Ozge Engin
> > --
> > 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!
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>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 1 Jun 2010 15:42:22 -0400
> From: "Nilesh Dhumal" <ndhumal at andrew.cmu.edu>
> Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found
> in rtp entry with 3 atoms while sorting atoms
> To: jalemkul at vt.edu, "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Message-ID:
> <4d7dd068352ed48ab70927d368ba8ab6.squirrel at webmail.andrew.cmu.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> I have addes the "CO" residue.
> Coordinate file
>
> REMARK Accelrys Discovery Studio PDB file
> REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010
> HETATM 1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00
> C
> HETATM 2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00
> O
> HETATM 3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00
> O
> END
>
> in ffopla.rtp file.
>
> [ CO ] ; mandatory
> [ ATOMS ] ; mandatory
> C1 opls_974 1.00 1
> O2 opls_975 -0.50 2
> O3 opls_976 -0.50 2
>
> [ bonds ]
> C1 O2
> C1 O3
>
> I have also addes new atoms typs in ffopls.atp file.
>
> NIlesh
>
> On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
> >
>
> >
> > Nilesh Dhumal wrote:
> >
> >> Hello,
> >>
> >>
> >> I am getting the following error during pdb2gmx.
> >>
> >>
> >> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms
> >> while sorting atoms
> >>
> >> I checked the pdb file and ffopls.rtp file also.
> >>
> >>
> >
> > And what did you find? To my knowledge there is no such residue "CO" in
> > the ffoplsaa.rtp file. Is this something you've added? Regardless,
> > there's a mismatch somewhere, so if you can't identify it, post the text
> > of your coordinate file and the relevant .rtp entry to see if someone
> else
> > can spot it.
> >
> > -Justin
> >
> >
> >> Nilesh
> >>
> >>
> >>
> >>
> >>
> >
> > --
> > ========================================
> >
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> >
> > ========================================
> > --
> > 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
> >
> >
> >
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 01 Jun 2010 16:17:21 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found
> in rtp entry with 3 atoms while sorting atoms
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4C056AD1.3000804 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Nilesh Dhumal wrote:
> > I have addes the "CO" residue.
> > Coordinate file
> >
> > REMARK Accelrys Discovery Studio PDB file
> > REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010
> > HETATM 1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00
> C
> > HETATM 2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00
> O
> > HETATM 3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00
> O
> > END
> >
> > in ffopla.rtp file.
> >
> > [ CO ] ; mandatory
> > [ ATOMS ] ; mandatory
> > C1 opls_974 1.00 1
> > O2 opls_975 -0.50 2
> > O3 opls_976 -0.50 2
> >
> > [ bonds ]
> > C1 O2
> > C1 O3
> >
> > I have also addes new atoms typs in ffopls.atp file.
> >
>
> These input files work fine for me. The error message complained about an
> atom
> named "O" so be sure you're using the input you think you are. Something
> has
> gotten confused somewhere.
>
> -Justin
>
> > NIlesh
> >
> > On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
> >
> >> Nilesh Dhumal wrote:
> >>
> >>> Hello,
> >>>
> >>>
> >>> I am getting the following error during pdb2gmx.
> >>>
> >>>
> >>> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms
> >>> while sorting atoms
> >>>
> >>> I checked the pdb file and ffopls.rtp file also.
> >>>
> >>>
> >> And what did you find? To my knowledge there is no such residue "CO" in
> >> the ffoplsaa.rtp file. Is this something you've added? Regardless,
> >> there's a mismatch somewhere, so if you can't identify it, post the text
> >> of your coordinate file and the relevant .rtp entry to see if someone
> else
> >> can spot it.
> >>
> >> -Justin
> >>
> >>
> >>> Nilesh
> >>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> ========================================
> >>
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >>
> >> ========================================
> >> --
> >> 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
> >>
> >>
> >>
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 02 Jun 2010 06:29:45 +1000
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found
> in rtp entry with 3 atoms while sorting atoms
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <fbb49af029bfd.4c05fa59 at anu.edu.au>
> Content-Type: text/plain; charset="us-ascii"
>
>
>
> ----- Original Message -----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Date: Wednesday, June 2, 2010 6:18
> Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in
> rtp entry with 3 atoms while sorting atoms
> To: Gromacs Users' List <gmx-users at gromacs.org>
>
> >
> > Nilesh Dhumal wrote:
> > >I have addes the "CO" residue.
> > >Coordinate file
> > >
> > >REMARK Accelrys Discovery Studio PDB file
> > >REMARK Created: Fri May 28 17:26:23 Eastern
> > Daylight Time 2010
> > >HETATM 1 C1
> > CO 0 -
> > 1.044 -0.027 0.066 0.00
> > 0.00 C
> > >HETATM 2 O2
> > CO 0 -
> > 0.009 0.642 -0.037 0.00
> > 0.00 O
> > >HETATM 3 O3
> > CO 0 -
> > 2.286 0.595 -0.030 0.00
> > 0.00 O
> > >END
> > >
> > >in ffopla.rtp file.
> > >
> > >[ CO ] ; mandatory
> > >[ ATOMS ] ; mandatory
> > > C1 opls_974 1.00 1
> > > O2 opls_975 -0.50 2
> > > O3 opls_976 -0.50 2
> > >
> > >[ bonds ]
> > > C1 O2
> > > C1 O3
> > >
> > >I have also addes new atoms typs in ffopls.atp file.
> > >
> >
> > These input files work fine for me. The error message
> > complained about an atom
> > named "O" so be sure you're using the input you think you
> > are. Something has
> > gotten confused somewhere.
>
> Perhaps the .pdb has column-formatting problems. Also, naming carbon
> dioxide "CO" and having two distinct atom types for its oxygen atoms, with
> non-neutral charge groups seems like asking for trouble...
>
> Mark
>
> >
> > -Justin
> >
> > >NIlesh
> > >
> > >On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
> > >
> > >>Nilesh Dhumal wrote:
> > >>
> > >>>Hello,
> > >>>
> > >>>
> > >>>I am getting the following error during pdb2gmx.
> > >>>
> > >>>
> > >>>Fatal error: Atom O in residue CO 1 not found in rtp entry
> > with 3 atoms
> > >>> while sorting atoms
> > >>>
> > >>>I checked the pdb file and ffopls.rtp file also.
> > >>>
> > >>>
> > >>And what did you find? To my knowledge there is no such
> > residue "CO" in
> > >>the ffoplsaa.rtp file. Is this something you've
> > added? Regardless,
> > >>there's a mismatch somewhere, so if you can't identify it,
> > post the text
> > >>of your coordinate file and the relevant .rtp entry to see if
> > someone else
> > >>can spot it.
> > >>
> > >>-Justin
> > >>
> > >>
> > >>>Nilesh
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>--
> > >>========================================
> > >>
> > >>
> > >>Justin A. Lemkul
> > >>Ph.D. Candidate
> > >>ICTAS Doctoral Scholar
> > >>MILES-IGERT Trainee
> > >>Department of Biochemistry
> > >>Virginia Tech
> > >>Blacksburg, VA
> > >>jalemkul[at]vt.edu | (540) 231-9080
> > >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >>
> > >>
> > >>========================================
> > >>--
> > >>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
> > >>
> > >>
> > >>
> > >
> > >
> > >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > 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
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> End of gmx-users Digest, Vol 74, Issue 13
> *****************************************
>
--
Ozge Engin
★☆
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