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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Sent: Tuesday, February 28, 2012 11:29 AM
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Subject: gmx-users Digest, Vol 94, Issue 173
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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)
----------------------------------------------------------------------
Message: 1
Date: Tue, 28 Feb 2012 21:10:49 +1100
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] A theoretical question
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="us-ascii"
On 28/02/12, "Du Jiangfeng (BIOCH)" <[email protected]> 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 <[email protected]>
Subject: Re: [gmx-users] adding a new residue type
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="us-ascii"
On 28/02/12, Banafsheh Mehrazma <[email protected]> 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 <[email protected]>
Subject: Re: [gmx-users] A theoretical question
To: [email protected]
Message-ID: <[email protected]>
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 [email protected]
> 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 [email protected].
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
------------------------------
Message: 4
Date: Tue, 28 Feb 2012 10:00:53 +0000
From: "Kukol, Andreas" <[email protected]>
Subject: [gmx-users] RE: A theoretical question
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<2f848dc922c8d741bf3a60b7d7108b6aa2627a5...@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: [email protected] [mailto:[email protected]] On
Behalf Of Du Jiangfeng (BIOCH)
Sent: 28 February 2012 09:46
To: [email protected]
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--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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Please don't post (un)subscribe requests to the list. Use the www interface or
send it to [email protected].
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