[gmx-users] RE: gmx-users Digest, Vol 94, Issue 173

Du Jiangfeng (BIOCH) j.du at maastrichtuniversity.nl
Tue Feb 28 11:47:41 CET 2012


Dear Mark, Javier and Andreas,

Thank you for your replies. Yes, I totally agree with all of you. There are really many advantages if separating the equilibration step apart from real MD simulation. As you guys mentioned: Variable parameters making the simulation more efficient and accurate; special constraint available ... 

Does the separated equilibration have other merits besides these?


    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands
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Today's Topics:

   1. Re: A theoretical question (Mark Abraham)
   2. Re: adding a new residue type (Mark Abraham)
   3. Re: A theoretical question (Javier Cerezo)
   4. RE: A theoretical question (Kukol, Andreas)


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Message: 1
Date: Tue, 28 Feb 2012 21:10:49 +1100
From: Mark Abraham <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] A theoretical question
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <77408b9e13230.4f4d42d9 at anu.edu.au>
Content-Type: text/plain; charset="us-ascii"



On 28/02/12, "Du Jiangfeng (BIOCH)" <j.du at maastrichtuniversity.nl> wrote:

> Dear GMX-users,
>
> In my impression, a conventional simulation should be composed by:  assemble system --> energy minimization --> NVT and NPT equilibration --> MD simulation, right? Now assume this procedure is correct, how about if there is no equilibration, as long as we set the temperature and pressure at the purposed numbers in MD parameter files?


If you do that, then the first chunk of your simulation will need to be discarded as part of an equilibration regime. Probably you should do that anyway, even if you have a section you *call* equilibration.

However, the real reason for having a separate equilibration part is that various algorithms and parameters are unsuitable for use in a non-equilibrated system. You want to change these later on to those more suitable for long-term use, so you should plan for that in advance.

Mark
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Message: 2
Date: Tue, 28 Feb 2012 21:17:45 +1100
From: Mark Abraham <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] adding a new residue type
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <7610c43310d92.4f4d4479 at anu.edu.au>
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On 28/02/12, Banafsheh Mehrazma <bmehrazma at gmail.com> wrote:

>
>  Dear all;
> I have used a modified guanine in my simulation before, with new parameters added in amber99 force field and there was no error through the whole simulation. now I'm trying to do a simulation with modified Guanine on a different sequence of the DNA with the same commands;
>
>                     pdb2gmx -f modified.pdb -o DNA.gro
>                      editconf -f DNA.gro -o DNA_newbox.gro -c -d 1.0 -bt cubic
>                      genbox -cp DNA_newbox.gro -cs spc216.gro -o DNA_solv.gro -p topol.top
> but when I run this one;
>                      grompp -f ions.mdp -c DNA_solv.gro -p topol.top -o ions.tpr
>  there is this error
>
>
>                 ERROR  [file topol_DNA_chain_A.itp, line 2304]:
>                 No default Angle types
>
> so when I checked the topology files,  I saw that for the next residue after the modified guanine, the O3' has a H3T (bonded to H terminal, which I don't know where this did came from) and another bond to P of modified guanine (which should have).  I guess, gromacs recognized it as a terminal base, however it has the linkage to the next base, as well.
>
>
> The only difference between my last dna and this one, is that in the last one the modification was in the 2nd position but this one is in the fourth.
>
>
> I think there may be a problem with my specbond.dat :
> .................................................................................................................................
>
> 9
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> CYS SG 1 HEM FE 2 0.25 CYS2 HEME
> CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
> CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
> HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
> MET SD 1 HEM FE 1 0.24 MET HEME
> CO      C       1       HEME    FE      1       0.19    CO      HEME
> CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
> 8OG P 2 DT O3' 2 0.161 8OG DT
>
> ...................................................................................................................................
> or maybe not. Any suggestions will be really appreciated. :)
>
>


We don't have enough information to suggest anything. If the only difference really is the order of non-terminal amino acids, then your symptoms seem impossible. You should look at line 2304 and work backwards.

Mark
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Message: 3
Date: Tue, 28 Feb 2012 11:02:11 +0100
From: Javier Cerezo <jcb1 at um.es>
Subject: Re: [gmx-users] A theoretical question
To: gmx-users at gromacs.org
Message-ID: <4F4CA623.9040006 at um.es>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Jiangfeng

Here you have my view on that topic:

You will alway have some equilibration time from a minimized structure,
no mater if you make it on a separate run or not. I mean, the system
will need some time to reach equilibrium conditions, and in case you
don't set separate runs for equilibration you will need to discard the
beginning of your production run until equilibrium is reached (you can
check energy, temperature, pressure...).

The point of making it in different steps is that you can play with the
conditions to make the equilibration process more efficient. For
example, a first NVT equilibration will (quickly) lead you to the target
temperature. Then an NpT equilibration will set the correct pressure. In
both equilibration steps you can use the Berendsen thermostat and
barostat with will efficiently drive your system to your selected
conditions. For production you can then switch to Nose-Hoover and
Parrinelo-Rahman if you are interested in getting a well defined
thermodynamic ensemble.

Javier

El 28/02/12 10:45, Du Jiangfeng (BIOCH) escribi?:
> Dear GMX-users,
>
> In my impression, a conventional simulation should be composed by:  assemble system -->  energy minimization -->  NVT and NPT equilibration -->  MD simulation, right? Now assume this procedure is correct, how about if there is no equilibration, as long as we set the temperature and pressure at the purposed numbers in MD parameter files?
> Actually, this is puzzling me always.
> Any reply is appreciated.
>
>
>      Jiangfeng Du, PhD Student
>      Cardiovascular Research Institute Maastricht
>      Department of Biochemistry
>      P.O. Box 616
>      Mobile: +31-681741859
>      FAX: +31-43-3884159
>      6200 MD Maastricht
>      The Netherlands--
> 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.
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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434


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Message: 4
Date: Tue, 28 Feb 2012 10:00:53 +0000
From: "Kukol, Andreas" <a.kukol at herts.ac.uk>
Subject: [gmx-users] RE: A theoretical question
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <2F848DC922C8D741BF3A60B7D7108B6AA2627A5B2A at UH-MAILSTOR.herts.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hello,

Firstly, proper equilibration is a technical requirement. The production MD simulation might crash, if the system was not properly equilibrated.

Secondly, if you want to study the properties of a macromolecule in solvent, you must do a macromolecule position-restraint equilibration. Otherwise, the structure of the macromolecule would be distorted in a non-natural way.

Best wishes
Andreas

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Du Jiangfeng (BIOCH)
Sent: 28 February 2012 09:46
To: gmx-users at gromacs.org
Subject: [gmx-users] A theoretical question

Dear GMX-users,

In my impression, a conventional simulation should be composed by:  assemble system --> energy minimization --> NVT and NPT equilibration --> MD simulation, right? Now assume this procedure is correct, how about if there is no equilibration, as long as we set the temperature and pressure at the purposed numbers in MD parameter files?
Actually, this is puzzling me always.
Any reply is appreciated.


    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands--
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