[gmx-users] simulation at higher temperatures gmx-users Digest, Vol 88, Issue 167
arun kumar
arunjones.kumar89 at gmail.com
Tue Aug 30 17:13:56 CEST 2011
hi justin, I accept with u that simulation will not complete in 3ns, but as
iam trying simulation at 400k for the first time i just kept it for 3ns to
see how it will be.
and for checking conformational changes i saved the structures for each
100ps from the trajectory (is it a correct procedure for that.....?)
and is it possible to give explanation for the parameters and forcefield
that we need to fallow for higher temperature simulations......?
On Mon, Aug 29, 2011 at 7:24 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: OPLS-AA Unknown Atomtype (Justin A. Lemkul)
> 2. Error found on grompp - energy minimization (ITHAYARAJA)
> 3. Re: Error found on grompp - energy minimization (Mark Abraham)
> 4. Re: gromacs question topologie (Justin A. Lemkul)
> 5. Re: Difficulty building a topology for a synthetic, branched
> PEG-peptide molecule [SOLVED] (Pablo Englebienne)
> 6. simulation at higher temperatures (arun kumar)
> 7. Re: simulation at higher temperatures (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Aug 2011 06:41:32 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E5B6CDC.8000103 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Yao Yao wrote:
> > Hi Justin,
> >
> > Thanks for your last reply. Now it seems that OPLS has known the
> > atomtypes after I added those CA1, ... to ffoplsaanb.itp,
> > but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp,
> > it still gives errors like,
> >
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> > checking input for internal consistency...
> > processing topology...
> > Opening library file
> /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> > Opening library file
> /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> > Opening library file
> > /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> > Generated 338253 of the 338253 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 338253 of the 338253 1-4 parameter combinations
> >
> > ERROR 1 [file cro.top, line 37]:
> > No default Bond types
> >
> >
> > ERROR 2 [file cro.top, line 71]:
> > No default Angle types
> >
> >
> > ERROR 3 [file cro.top, line 72]:
> > No default Angle types
> >
> >
> > ERROR 4 [file cro.top, line 85]:
> > No default Angle types
> >
> >
> > ERROR 5 [file cro.top, line 91]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 6 [file cro.top, line 92]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 7 [file cro.top, line 93]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 8 [file cro.top, line 108]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 9 [file cro.top, line 112]:
> > No default Proper Dih. types
> >
> >
> > ERROR 10 [file cro.top, line 113]:
> > No default Proper Dih. types
> >
> >
> > ERROR 11 [file cro.top, line 114]:
> > No default Proper Dih. types
> >
> > Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
> > Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
> > Excluding 3 bonded neighbours molecule type 'Protein'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> >
> > NOTE 1 [file cro.top, line 142]:
> > System has non-zero total charge: -1.022478e+00
> >
> >
>
> This total charge suggests that your topology is badly broken.
>
> >
> > processing coordinates...
> > double-checking input for internal consistency...
> > renumbering atomtypes...
> > converting bonded parameters...
> >
> > There was 1 note
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 4.0.7
> > Source code file: grompp.c, line: 986
> >
> > Fatal error:
> > There were 11 errors in input file(s)
> > -----------------------------------------------
> >
> > I do double-check those bondtypes, angles, and interactions mentioned in
> > the errors, and I am pretty sure I have already declared those values in
> > the ffoplsaabon.itp.
> > Is there any other file I also need to mention those values?
> >
>
> If these types were actually present in ffoplsaabon.itp, then you wouldn't
> get
> these errors. Double check again.
>
> -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: 2
> Date: Mon, 29 Aug 2011 16:48:36 +0530
> From: ITHAYARAJA <ithayaraja at gmail.com>
> Subject: [gmx-users] Error found on grompp - energy minimization
> To: gmx-users at gromacs.org
> Message-ID:
> <CA+kBMrN7Ok_-JctVNVTA8GA05g_dhzPo585GUuB_8Li=FhNWXQ at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear sir,
> I struck with the following error when i perform energy minimization. I
> unable to understand what did it mean? please make me clear.
>
> So kindly do the needful.
>
> Fatal error:
> Atomtype CR1 not found
>
> --
> **
> Ithayaraja M,
> Research Scholar,
> Department of Bionformatics,
> Bharathiar University,
> Coimbatore 641 046,
> Tamil Nadu
> India
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> ------------------------------
>
> Message: 3
> Date: Mon, 29 Aug 2011 21:22:53 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Error found on grompp - energy minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E5B768D.206 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 29/08/2011 9:18 PM, ITHAYARAJA wrote:
> > Dear sir,
> > I struck with the following error when i perform energy minimization.
> > I unable to understand what did it mean? please make me clear.
> >
> > So kindly do the needful.
> >
> > Fatal error:
> > Atomtype CR1 not found
>
> One of your molecules is trying to use an atomtype that isn't defined in
> your force field. However we can't guess why without a lot more
> information. See http://www.gromacs.org/Support
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 29 Aug 2011 08:49:18 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: [gmx-users] Re: gromacs question topologie
> To: Joschua Sterzenbach <joschua_s at yahoo.de>, Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E5B8ACE.8010609 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
> Please keep all Gromacs-related correspondence on the gmx-users list,
> particularly if the discussion was previously carried out there. I am not
> a
> private tutor.
>
> Joschua Sterzenbach wrote:
> > Hi
> >
> > is in the coordinate file only the geometry of the molecule?
> >
>
> Yes. Have a look at its contents - all you'll find in most common formats
> are
> the (x,y,z) coordinates of the named atoms.
>
> > I ask because I only have the geometry.
> >
> > Do I get the topologie out of the geometry or from where comes it?
> >
>
> Please do some basic tutorial material to understand the Gromacs workflow.
> For
> residue-based biomolecules like proteins and nucleic acids, use pdb2gmx.
> For
> other molecules, g_x2top can create basic topologies for a limited number
> of
> force fields and molecules. Otherwise, you'll have to obtain the topology
> by
> some other means. There are other programs on the User Contributions page
> of
> the Gromacs site that can produce topologies for arbitrary molecules.
>
> You haven't said yet what you're working with, so all I can do is venture
> guesses.
>
> -Justin
>
> > The questions corresponds to this:
> > http://www.mail-archive.com/gmx-users@gromacs.org/msg43478.html
> >
> > Thanks
> > Regards
>
> --
> ========================================
>
> 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: Mon, 29 Aug 2011 15:02:30 +0200
> From: Pablo Englebienne <p.englebienne at tue.nl>
> Subject: [gmx-users] Re: Difficulty building a topology for a
> synthetic, branched PEG-peptide molecule [SOLVED]
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID: <4E5B8DE6.5050901 at tue.nl>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> > That's a long bond. Does your reference length in specbond.dat suit it?
> > IIRC there should be some evidence in the output of the special bond
> > being formed if it actually is. If not, your symptoms are probably
> related
> Hi Mark, indeed, I think that was part of the problem. pdb2gmx indeed
> outputs a message when a specbond.dat rule is matched and a bond formed.
>
> In case it helps to someone else or for reference purposes, I finally
> managed to solve the issue.
>
> Some of the lessons I learned:
> - make sure that the residues/atoms in specbond.dat were correct (I had
> defined a number of residues for termini and mid-chain PEG and
> connectors, and I got them confused at some point, so not all of them
> were being recognized properly). The "dangling bond at at least one of
> the terminal ends" given by pdb2gmx is most likely due to this and/or
> the protonation state of the residues connecting the fragments
> - each fragment is assigned a different chain letter in the source PDB
> file; in my case, for a system like
>
> [N-(peptide1)-C]-[N-(PEG)-C]-[N-(peptide2)-Lys-C]
> |
> NZ
> |
> [C-(PEG)-N]-[C-(peptide3)-N]
>
> each fragment in square brackets is assigned a different chain name in
> [A-E] in the PDB file:
>
> ATOM 123 N ARG A 1 74.024 13.299 50.237 1.00
> 0.00 N1+
> ^
> - always list the atoms within a chain in an N-to-C direction. This
> means that the main branch is defined first, and then the branching
> point is defined in an N-to-C direction, even if it is counterintuitive
> by the way they are connected. specbond.dat takes good care of setting
> up the connection in all cases (as long as they are well defined...).
> - the PEG residues need to be defined as type "Other" in residues.dat
> - call pdb2gmx to manually assign the termini and Lys protonation states
> manually, and to merge the chains into a single molecule:
>
> pdb2gmx-ter -f substrate.pdb-chainsep interactive-lys
>
> -> the "internal" termini (i.e., the ones that are peptide termini but
> are connected to a PEG chain) need to be given a protonation state of
> "None", while the "real" termini can be assigned as charged or neutral,
> depending on the conditions
>
> > Oh, and well done for constructing a good question. You would likely not
> have gotten anywhere giving less detail :)
> Thanks, it actually helped putting everything in writing, as it pointed
> out the few things that I hadn't yet looked at in detail...
>
> Pablo Englebienne, PhD
> Dept. of Biomedical Engineering
> Dept. of Chemistry and Chemical Engineering
> Institute for Complex Molecular Systems (ICMS)
> Eindhoven University of Technology, TU/e
> PO Box 513, HG -1.26
> 5600 MB Eindhoven, The Netherlands
> Tel +31 40 247 5349
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 29 Aug 2011 19:19:36 +0530
> From: arun kumar <arunjones.kumar89 at gmail.com>
> Subject: [gmx-users] simulation at higher temperatures
> To: gmx-users at gromacs.org
> Message-ID:
> <CAGM9vJ_iBDbQpnEkTdKYQyu2kaAz1Gqb3wL-UYv_06Lj=beh0w at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi friends,
>
> As a part of my work i have to do simulation at higher temperature (400K or
> more) to study the folding, unfolding and stability of protein, for that i
> kept simulation for 3ns at 400k (400k temperature both in equilibration and
> production) keeping all the other parameters as usual (time step 2fs,
> explicit solvent model SPC, equilibration with NVT and NPT ensembles for
> 100ps each ). the simulation was completed but ,
> 1. in trajectory i found that protein is comming out of the box (cubic box
> -d 1.0) i think may be the box size was not sufficient (and i know that
> when we increase the temperature the velocity of atoms will increase).
> 2. when i save the structure with minimum energy and saw in pymol i found
> the side chains, hydrogens was broken through out the protein.
> 3. later i used the command ( trajconv -s md.tpr -f md.trr -o protein.pdb
> -pbc nojump -dt 10 ) to save the conformations at each 10 ps and to see the
> conformational changes by playing it as a movie in pymol , but i found a
> single conformation was just shaking through out the movie (this is
> happening in normal simulation also)
>
> later i read in gmx user problems that most of the force field parameters
> are calculated at room temperature, so in that case what are the parameters
> and forcefield that we need to fallow for higher temperature simulations.
>
> so can any one please takes time to explain this, it would be helpful for
> me
> to study further.
>
> Thanking you.
>
> with regards
> --
> Arun Kumar Somavarapu
> Center for Bioinformatics
> Pondicherry University
> Kalapet
> Puducherry-605014
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> ------------------------------
>
> Message: 7
> Date: Mon, 29 Aug 2011 09:53:45 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] simulation at higher temperatures
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E5B99E9.7060504 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> arun kumar wrote:
> >
> > Hi friends,
> >
> > As a part of my work i have to do simulation at higher temperature (400K
> > or more) to study the folding, unfolding and stability of protein, for
> > that i kept simulation for 3ns at 400k (400k temperature both in
> > equilibration and production) keeping all the other parameters as usual
> > (time step 2fs, explicit solvent model SPC, equilibration with NVT and
> > NPT ensembles for 100ps each ). the simulation was completed but ,
>
> I doubt any simulation, even of the simplest protein, is "complete" at 3
> ns.
>
> > 1. in trajectory i found that protein is comming out of the box (cubic
> > box -d 1.0) i think may be the box size was not sufficient (and i know
> > that when we increase the temperature the velocity of atoms will
> increase).
>
> Please see FAQ #3 under the following section:
>
> http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization
>
> > 2. when i save the structure with minimum energy and saw in pymol i
> > found the side chains, hydrogens was broken through out the protein.
>
> Same as above.
>
> > 3. later i used the command ( trajconv -s md.tpr -f md.trr -o
> > protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps
> > and to see the conformational changes by playing it as a movie in pymol
> > , but i found a single conformation was just shaking through out the
> > movie (this is happening in normal simulation also)
>
> Your simulation length is inadequate to view any conformational changes.
> These
> types of motions can require hundreds of ns, if not more (depending on the
> size
> of the protein), to visualize.
>
> -Justin
>
> >
> > later i read in gmx user problems that most of the force field
> > parameters are calculated at room temperature, so in that case what are
> > the parameters and forcefield that we need to fallow for higher
> > temperature simulations.
> >
> > so can any one please takes time to explain this, it would be helpful
> > for me to study further.
> >
> > Thanking you.
> >
> > with regards
> > --
> > Arun Kumar Somavarapu
> > Center for Bioinformatics
> > Pondicherry University
> > Kalapet
> > Puducherry-605014
> >
>
> --
> ========================================
>
> 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!
>
> End of gmx-users Digest, Vol 88, Issue 167
> ******************************************
>
--
Arun Kumar Somavarapu
Center for Bioinformatics
Pondicherry University
Kalapet
Puducherry-605014
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