Hi Una,
That seems perfectly sensible. The only thing is that I'd use editconf
for renumbering, but I'm not even sure whether that will actually make
a difference.
Best,
Tsjerk
On 10/11/06, Una Bjarnadottir <[EMAIL PROTECTED]> wrote:
Thank you so much for your response Viswanadham Sridhara an
hello everyone
i want to know can i change or control the solvent size:my system is composed of two monolayers,and i want to add solvent just bettwen the monolayers!
can anyone help me ?thanks addvaced!
美 女 恐 怖 败 家 秀 ( 组 图 )
独 家 披 露 ! 小 资 女 人 8 个 绝 顶 隐 秘 的 趣 事 ( 组 图 )
__
Sounds like you you're using an old version of g_hbond. Either get a fresher
version of gmx_hbond from the cvs repository or use g_hbond -nomerge. The
latter generates unmerged hbn/hbm output that match. Look through the
mailinglists.
/Erik
- Original Message -
From: "merc mertens" <
Title: mixed solvent minimization
Hello Gromacs Users,
I am trying to equilibrate a box that contains TFE and TIP4P water molecules using the OPLSAA/L force field. The system converged several times using the steepest descent method, but each time I attempted a full simulation I received th
Anton Feenstra wrote:
Mark Abraham wrote:
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1180
Fatal error:
Incorrect number of parameters - found 4, expected 6 or 12.
-
Hi,
On Oct 9, 2006, at 5:38 PM, Anton Feenstra wrote:
Nevertheless, on newer architectures, threads would ultimately be
the better choice. They're working on it and according to David van
der Spoel it will be in 4.0 (that was on the Developer's list in
May '04... Br, as David would p
Mark Abraham wrote:
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1180
Fatal error:
Incorrect number of parameters - found 4, expected 6 or 12.
---
This is being cause
Mark Abraham wrote:
Samuel Silva Pita wrote:
Hi GMXers,
how can I find the names of the molecules that are represented at rtp
archives?
I'd tried to see at aminoacids.dat and at *bond.itp but I cannot find
the names. For example: ETH, BA, ETHH, RTOL. Which molecules are these?
Umm, residue
Jake Michaelson wrote:
Another problem I've run into (this is OT) is the '--enable-threads'
option. I know (from other mailing list posts) that this doesn't work
in any of the releases, but how about CVS? If it doesn't work, why
include the option in the configure script? It seems like with t
HI Users:
I want to rerun my system to determine the energy of the protein. What I need
to do?
If the answer is to set up energygrp_excl I could include all the component of
the system except the protein in one
group an use this group for the energygrp_excl because my system have 6
differe
Thank you so much for your response Viswanadham Sridhara and Tsjerk
Wassenaar Still I seem to be doing something wrong because the ions
always end up in the active site cleft!. This is what I do: 1. I move
the 2 watermolecules (all three atoms) which I don't want to be replaced
at the bottom of
hello,
after using g_hbond to generate an *.xpm file one sees in the *.xpm file the
following: "y-label: "Hydrogen Bond Index"" and the y-axis ranges between 0 and
163. if i look in the additionally generated hbbond.ndx file, i see at the
bottom of it the group "[ hbonds_* ]". i assumed that th
Reynier Suardiaz del Rio wrote:
i want to performe a MD of a small systems with gromos, i would like to
obtain new parameters for this system.
the systems have two or three dihedrals.
i want to fix C6 and C12 of 1-4 interactions for reproduction of quantum
potential energy surface obtained fr
i want to performe a MD of a small systems with gromos, i would like to
obtain new parameters for this system.
the systems have two or three dihedrals.
i want to fix C6 and C12 of 1-4 interactions for reproduction of quantum
potential energy surface obtained from the simultaneous change of the
Dallas B. Warren wrote:
> Gavin,
>
>> I have created my topology file but when I run pdb2gmx it
>> complains of a missing rtp file. Will someone outline how I
>> use pdb2gmx when the topology for my protein is not in the
>> top dir? Gavin
>
> You don't.
>
> pdb2gmx only works when the forcef
Hi... I read the FAQ on using gromacs with FFTW...
I set the LD_LIBRARY_PATH, yet when trying to make gromacs, at the ./
configure point, it still complains about not being able to find fftw
configure: error: Cannot find fftw3f library
ls /usr/local/lib/*fftw*
/usr/local/lib/libfftw.a /usr/loc
Can gromacs make use of xgrid on mac os x?
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Brian O'Brien wrote:
Hi... I read the FAQ on using gromacs with FFTW...
I set the LD_LIBRARY_PATH, yet when trying to make gromacs, at the ./
configure point, it still complains about not being able to find fftw
configure: error: Cannot find fftw3f library
ls /usr/local/lib/*fftw*
/usr/local/l
Hi... I read the FAQ on using gromacs with FFTW...
I set the LD_LIBRARY_PATH, yet when trying to make gromacs, at the ./
configure point, it still complains about not being able to find fftw
configure: error: Cannot find fftw3f library
ls /usr/local/lib/*fftw*
/usr/local/lib/libfftw.a /usr/loc
On 10/11/2006 1:57 PM, Mark Abraham wrote:
As an aside, I did develop assembly innerloops for CHARMM TIP3P water
for x86 some time back and posted here. My main compute platform isn't
x86 though, so I've not used them in anger. See discussions back in
Feb and March this year on gmx-developers.
Hi Mark,On Oct 11, 2006, at 7:57 AM, Mark Abraham wrote: Mostly correct - non-CHARMM TIP3P has LJ on the oxygen. However, the decision about which code to use is made on-the-fly by mdrun. If the molecule matches the pattern of a water molecule and only has LJ parameters on the oxygen then the optim
21 matches
Mail list logo
