[gmx-users] Re: gmx-users Digest, Vol 83, Issue 160
Kishore
kris.vempali at gmail.com
Sat Mar 26 18:39:01 CET 2011
Dear Mark,
As you correctly pointed out, I had looked into those improper dihedral
specifications several times before and it seems that they are properly
mentioned in the .itp file. I have been using the topologies generated by
PRODRG server for NADPH as i could not make it comply with the inbuilt
residue template library topologies. In this topologies generated by PRODRG
there is a directive called [ dihedrals ] and it listed out all the
dihedrals with comment lines showing proper and improper dihedrals, but this
seems to differ from the way the the topologies are defined in the gromacs
inbuilt template library which only lists out the impropers. Does this make
any difference in terms of grompp interpreting them during the
preprocessing? I am herein pasting a section of that dihedrals and a
snapshot of the NADPH molecule with the atom names labelled so that you can
see that the impropers you mentioned in your reply are infact mentioned in
the .itp file I am using.
The three improper dihedrals you have mentioned are highlighted
below...please correct me in case if i am getting the meaning wrong..Sorry
for flooding with long posts, but I am in a great need for some help on
this.
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 4 3 2 2 0.0 167.4 0.0 167.4 ; imp NBS CBQ
H8M HBS
4 1 5 6 2 0.0 167.4 0.0 167.4 ; imp CBQ NBS
OBT CAV
6 4 9 7 2 0.0 167.4 0.0 167.4 ; imp CAV CBQ
CBE CAN
On Wed, Mar 23, 2011 at 8:37 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Alcohol Dehydrogenase MD simulation....Reg (Mark Abraham)
> 2. Re: Parameterization of a molecule containing a radical
> (oxygen) (Justin A. Lemkul)
> 3. unit of surface tension, KJ/mol? (Elisabeth)
> 4. Re: unit of surface tension, KJ/mol? (Justin A. Lemkul)
> 5. Re: unit of surface tension, KJ/mol? (Elisabeth)
> 6. Re: unit of surface tension, KJ/mol? (Justin A. Lemkul)
> 7. Re: unit of surface tension, KJ/mol? (Elisabeth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 Mar 2011 11:46:30 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Alcohol Dehydrogenase MD simulation....Reg
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D8942E6.8020104 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 23/03/2011 4:38 AM, Kishore wrote:
> > Dear All,
> >
> > I had been in the look out for someone who has a reasonable amount of
> > expertise in dealing with the MD simulation of an Alcohol
> > Dehydrogenase. I have a problem dealing with the NADPH. I was unable
> > to maintain the planarity of the carboxamide of the nicotinamide
> > moiety in the simulation as a result of which important sidechain
> > hydrogen bonds are being lost in the simulation. Is such behaviour
> > expected or is it because of the non quantum mechanical treatment of
> > the NADPH molecule that these kind of situations occur? If anyone has
> > some experience please share it.
>
> Classical MD simulations use improper dihedrals to maintain such
> planarity. You can see this in the amide links in a peptide backbone,
> for example. Each set of four co-planar atoms (three arranged around a
> central one) needs an improper dihedral. So you need H-N-C-H, N-C-O-Cr4
> and C-Cr4-Cr5-Cr3 (where the ring carbons are named Cr and numbered
> clockwise from N) in order for the carboxamide to stay coplanar with the
> aromatic ring
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 22 Mar 2011 20:56:41 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Parameterization of a molecule containing a
> radical (oxygen)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D894549.80402 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Simone Cirri wrote:
> > Hi all,
> > I have a question regarding a new parameterization: actually, I'm
> > wondering whether or not it is possible to do it.
> >
> > The molecule is tempol; you cand find its PubChem entry
> > here
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs
> > <
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs>
> > As you can see, the problem of this molecule is its O radical; this, and
> > the N belonging to the cycle too.
> > My lab would really benefit from the parameterization (for the AMBER
> > force field) of tempol, since we commonly use it in our NMR experiments.
> > We don't know how to treat the oxygen radical and the N bound to it,
> though.
> > If this parameterization is impossible to do we will give up, but we
> > would like to be sure about it.
> > Thanks in advance for any answer you could provide.
> > <
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs>
>
> This would not be a trivial molecule to parameterize. You could start by
> using
> antechamber (available free as part of AmberTools), since it allows you to
> tune
> multiplicity (-m flag). Otherwise, the existing force fields may not
> provide a
> suitable atom type for the O radical or its effects on the rest of the
> molecule.
> I still don't know if parameterization would be possible for a standard MM
> force field (though it very well might), but this might get you started.
>
> -Justin
>
> > --
> >
> > Simone Cirri
> >
>
> --
> ========================================
>
> 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: 3
> Date: Tue, 22 Mar 2011 22:25:22 -0400
> From: Elisabeth <katesedate at gmail.com>
> Subject: [gmx-users] unit of surface tension, KJ/mol?
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTinmrO8APJhiM0Mef_uUvf604ge89gX9agZR3SbT at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I did two simulations on the same system using versions 4.0.7 and 4.5.3. It
> seems like the unit of surface tension is not the same in these versions
> because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?!
> How
> KJ/mol can be converted into bar nm? Can anyone help please.
>
> Thanks
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> ------------------------------
>
> Message: 4
> Date: Tue, 22 Mar 2011 22:31:12 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] unit of surface tension, KJ/mol?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D895B70.7080604 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Elisabeth wrote:
> > Hello,
> >
> > I did two simulations on the same system using versions 4.0.7 and 4.5.3.
> > It seems like the unit of surface tension is not the same in these
> > versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm
> > in 4.5.3?! How KJ/mol can be converted into bar nm? Can anyone help
> please.
> >
>
> Is this from g_energy output? In past versions, everything was printed as
> "kJ/mol," even quantities that obviously weren't, like temperature,
> pressure, etc.
>
> -Justin
>
> > Thanks
> >
>
> --
> ========================================
>
> 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: 5
> Date: Tue, 22 Mar 2011 22:44:04 -0400
> From: Elisabeth <katesedate at gmail.com>
> Subject: Re: [gmx-users] unit of surface tension, KJ/mol?
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTimqCrSrJMB3E1WzO2rYG=rVOhXVDSZEbLhvz4wu at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 22 March 2011 22:31, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > Elisabeth wrote:
> >
> >> Hello,
> >> I did two simulations on the same system using versions 4.0.7 and
> 4.5.3.
> >> It seems like the unit of surface tension is not the same in these
> versions
> >> because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?!
> How
> >> KJ/mol can be converted into bar nm? Can anyone help please.
> >>
> >>
> > Is this from g_energy output? In past versions, everything was printed
> as
> > "kJ/mol," even quantities that obviously weren't, like temperature,
> > pressure, etc.
> >
>
> Yes, so why are the results so different. I am using exactly the same mdp
> file.!
>
> >
> > -Justin
> >
> > Thanks
> >>
> >>
> > --
> > ========================================
> >
> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
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> ------------------------------
>
> Message: 6
> Date: Tue, 22 Mar 2011 22:46:08 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] unit of surface tension, KJ/mol?
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4D895EF0.9090505 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Elisabeth wrote:
> >
> >
> > On 22 March 2011 22:31, Justin A. Lemkul <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > Elisabeth wrote:
> >
> > Hello,
> > I did two simulations on the same system using versions 4.0.7
> > and 4.5.3. It seems like the unit of surface tension is not the
> > same in these versions because I am getting ~250 KJ/mol an in
> > 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
> > into bar nm? Can anyone help please.
> >
> >
> > Is this from g_energy output? In past versions, everything was
> > printed as "kJ/mol," even quantities that obviously weren't, like
> > temperature, pressure, etc.
> >
> >
> > Yes, so why are the results so different. I am using exactly the same
> > mdp file.!
> >
> >
>
> Any pressure-related quantity is going to be subject to enormous
> fluctuations.
> This has been discussed within the last few days. Without seeing the .mdp
> file
> and a description of the system, it's hard for anyone to comment on what
> the
> results might mean.
>
> -Justin
>
> --
> ========================================
>
> 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: 7
> Date: Tue, 22 Mar 2011 23:06:59 -0400
> From: Elisabeth <katesedate at gmail.com>
> Subject: Re: [gmx-users] unit of surface tension, KJ/mol?
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTim2ChGCp4ai_PwOPj19wHKkoaoyZhwSMQuGoO4b at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 22 March 2011 22:46, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > Elisabeth wrote:
> >
> >
> >>
> >> On 22 March 2011 22:31, Justin A. Lemkul <jalemkul at vt.edu <mailto:
> >> jalemkul at vt.edu>> wrote:
> >>
> >>
> >>
> >> Elisabeth wrote:
> >>
> >> Hello,
> >> I did two simulations on the same system using versions 4.0.7
> >> and 4.5.3. It seems like the unit of surface tension is not the
> >> same in these versions because I am getting ~250 KJ/mol an in
> >> 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
> >> into bar nm? Can anyone help please.
> >>
> >>
> >> Is this from g_energy output? In past versions, everything was
> >> printed as "kJ/mol," even quantities that obviously weren't, like
> >> temperature, pressure, etc.
> >>
> >>
> >> Yes, so why are the results so different. I am using exactly the same
> mdp
> >> file.!
> >>
> >>
> > Any pressure-related quantity is going to be subject to enormous
> > fluctuations. This has been discussed within the last few days. Without
> > seeing the .mdp file and a description of the system, it's hard for
> anyone
> > to comment on what the results might mean.
> >
>
> Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is
> extended in Z to create liq/air interface. That is 3X3X6 . What could be
> reason for such a big difference in results from two version? Thanks alot!
>
>
> integrator = md
> dt = 0.002
> nsteps = 1000000
>
> nstenergy = 100
> nstxout = 100
> nstlist = 10
> ns_type = grid
> coulombtype = PME
> vdw-type = Shift
> rcoulomb-switch = 0
> rvdw-switch = 0
> rlist = 1.1
> rcoulomb = 1.1
> rvdw = 1.0
>
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> ;optimize_fft = yes
>
> Tcoupl = v-rescale
> tc-grps = System
> tau_t = 0.1
> ref_t = 300
>
> pbc = xyz
>
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> constraints = all-bonds
> constraint-algorithm = lincs
>
>
> >
> > -Justin
> >
> >
> > --
> > ========================================
> >
> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
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> End of gmx-users Digest, Vol 83, Issue 160
> ******************************************
>
--
KRISHNA KISHORE at IIT-MADRAS
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