liang wrote:
Dear Mark,
Thanks for your advice, but from my understanding, Berger's force field
is based on OPLS/Amber.
Lipid itp files from Tieleman's website just use the atom type
definitions from GROMOS87.
And GROMOS87 is out of fashion now.
So thats why i think it would be better to use
Dear Mark,
Thanks for your advice, but from my understanding, Berger's force field is
based on OPLS/Amber.
Lipid itp files from Tieleman's website just use the atom type definitions
from GROMOS87.
And GROMOS87 is out of fashion now.
So thats why i think it would be better to use OPLS for prote
- Original Message
From: maite lopez cabezas <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Sunday, November 25, 2007 10:48:31 AM
Subject: Re: [gmx-users] area by lipid
Well I know that the x/y directions are scaled isotropically and the z
direction is scaled independien
On Sun, 25 Nov 2007 19:00:47 +0200
"OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
Hi all,
I am performing a REMD simulation in vacuum. Although I minimized the energy
of each initial replica by using a stringent convergence criterion, after the
the third attempt, the system exploided because of a hu
Hi all,
I am performing a REMD simulation in vacuum. Although I minimized the energy of
each initial replica by using a stringent convergence criterion, after the the
third attempt, the system exploided because of a huge deviation in the Lincs
algorithm.
Although I started to the simulation vi
Hi all,
I am performing a REMD simulation in vacuum. Although I minimized the energy of
each initial replica by using a stringent convergence criterion, after the the
third attempt, the system exploided because of a huge deviation in the Lincs
algorithm.
Although I started to the simulation vi
Yes, I used GROMOS87. Although it's deprecated now and I'm not sure
which ff to switch to.
Hadas.
On Sun, 2007-11-25 at 19:03 +0800, liang wrote:
> Hi Hadas,
>
> i have tried to use gromos87 for protein, everything is ok. (just with
> ffgmx.itp)
> but if i use opls for protein, i have to add "
> Hi Liang,
>
> Do you have to define ffoplsaa.itp in your top file? isn't it enough to
> generate your protein topology with the OPLS forcefield using pdb2gmx and
> include the protein's generated itp files?
No, because the .itp file is not self-contained. It is a topology for use
with a particul
> Dear Justin,
>
> Thanks for you quickly reply.
>
> I have tried before to comment out the section of [ defaults ] in the next
> itp file, but still too many warnings and final crashed.
> And i think it would not be the best method to solve this problem, because
> i
> have to use ffgmx.itp to deal
> Dear Gromacs users,
>
> When I tried to build up .tpr file for running energy minimisation, I
> encountered some problems:
>
> This is the command I used:
>
>
> grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr
>
>
> and I received the following error message:
>
> Fatal error:
> Invalid order
Hi Hadas,
i have tried to use gromos87 for protein, everything is ok. (just with
ffgmx.itp)
but if i use opls for protein, i have to add "ffoplsaa.itp" in top file,
otherwise it cannot provide some parameters for protein.
Did you use gromos87 to generate your protein itp files (chain_A .itp ...)
Well I know that the x/y directions are scaled isotropically and the z
direction is scaled independiently, and i must give just 2
compresibility valors, but people don't give this valor in the most of
the papers about membrane simulations. For example i use
on DPPC membrane
compressibility
Hi,
Maybe it's good to note that gromacs (mdrun) will always write the
coordinates such that the first atom of each molecule is located inside the
rectangular box spanned by the xx, yy and zz components of the triclinic
box, located at the origin.
Tsjerk
On Nov 25, 2007 4:47 AM, Mark Abraham <[E
Hi Jestin,
Read chapter 5 thoroughly :)
It seems that in your topology file (minding the #includes) the directive [
system ] is given too early, e.g. before the definition of the [
moleculetypes ].
Tsjerk
On 25 Nov 2007 05:51:50 -, JMandumpal <[EMAIL PROTECTED]> wrote:
> Dear Gromacs users,
Q733 wrote:
Dear gmx-users, I want to develop an itp file for an organic molecule
which has 87 atoms. I deduced the charge using the common Resp
procedure with RED-III tool.However , I am not quite sure if the Resp
charge or Esp charge can be used in Gromos forcefield, if not, how does
Gromos
Myunggi Yi wrote:
I have tested with 8, 16, 24 and 32 cpus.
Only parallel with 8 and 16 cpus works, and the other cases (24 and
32) are even much slower than 8 cpus' case.
Any idea about this?
larger systems
check mailing list
use 16 cpus until gmx 4
On Nov 24, 2007 11:42 AM, David van der
Hi Liang,
Do you have to define ffoplsaa.itp in your top file? isn't it enough to
generate your protein topology with the OPLS forcefield using pdb2gmx and
include the protein's generated itp files?
I don't use OPLS, but my own definition of the .top file goes like this:
; generic + lipid to
Dear gmx-users, I want to develop an itp file for an organic molecule which has
87 atoms. I deduced the charge using the common Resp procedure with RED-III
tool.However , I am not quite sure if the Resp charge or Esp charge can be used
in Gromos forcefield, if not, how does Gromos forcefied dedu
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