Hello, my configure line is ./configure --without-X
--enable-mpi --enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have
been setted in the ~/.bashrc like this :
export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin
export CC=gcc
export CXX=g++
export CFLAGS="-03
x
You have to rerun the trajectory ... not frame by frame!
Notes:
- that there is issue on pressure tensor calculation when constrains are
used
- simulations need to be quite long to get a reasonable convergence.
On Apr 12, 2010, at 2:41 AM, George Khelashvili wrote:
Dear users,
I am attemptin
kecy...@sina.com wrote:
Hello, my configure line is ./configure --without-X --enable-mpi
--enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have been
setted in the ~/.bashrc like this :
--without-X and --without-x are different things. Computers are literal. Watch
the outp
kecy...@sina.com wrote:
the version of the gcc is 4.1.1.
Get a better version of gcc. Note the prominent warning on the Downloads page:
http://www.gromacs.org/index.php?title=Download_%26_Installation
-Justin
Thank you!
--
Justin A. Lemkul
Dear Gromacs users:
I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when
carryied EM with Strong POStion REStraint, the protien and membrane were apart.
Please help me!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gm
xi zhao wrote:
Dear Gromacs users:
I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but
when carryied EM with Strong POStion REStraint, the protien and membrane
were apart. Please help me!
What does "apart" mean? If you want free help, you have to make it easy to help
yo
On 12/04/2010 10:37 PM, xi zhao wrote:
Dear Gromacs users:
I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but
when carryied EM with Strong POStion REStraint, the protien and membrane
were apart. Please help me!
Either you put them apart, or you're seeing a periodicity artefa
protein and membranr separate ,
--- 10年4月12日，周一, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and
inflategro.pl
收件人: "Discussion list for GROMACS users"
日期: 2010年4月12日,周一,下午8:42
xi zhao wrote:
>
>
> Dear Gromacs users:
my procesure:
1. cat cgprotein cgmembrane>system.gro (using Martini force field)
2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
3. grompp_d -f em.mdp -c system_inflated.gro -p topol.top -o
system_inflatedem.tpr (with strong postion restraint)
4. mdrun
5 in the system_in
xi zhao wrote:
my procesure:
1. cat cgprotein cgmembrane>system.gro (using Martini force field)
Were these structures initially centered within the same coordinate system? By
your description, it sounds like these two components are simply not placed
properly. There is a membrane protein
Dear Sir : In fact, these structures were initially centered within the same
coordinate system as your Gromacs Tutorials .
--- 10年4月12日，周一, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and
inflategro.pl
收件人: "Gromacs Users'
xi zhao wrote:
Dear Sir : In fact, these structures were initially centered within the
same coordinate system as your Gromacs Tutorials .
Then surely you made some sort of modification to the inflategro.pl script in
order to make it work with a CG structure, right? The standard script
Hello, the error is like that :
*In file included from ngmx.c:50:*
>
> *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory*
>
> *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory*
>
> *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory*
>
> *Xstuff.h:52:27: err
Thank you!
I will follow your guidelines.
George
XAvier Periole wrote:
You have to rerun the trajectory ... not frame by frame!
Notes:
- that there is issue on pressure tensor calculation when constrains are
used
- simulations need to be quite long to get a reasonable convergence.
On Apr 12
On 13/04/2010 12:14 AM, kecy...@sina.com wrote:
Hello, the error is like that :
*In file included from ngmx.c:50:*
>
> *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory*
>
> *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory*
>
> *Xstuff.h:51:28: error: X11/cursorfo
Hi everybody,
In order to use an old set of analysis programs, I would like mdrun to
ouput my trajectory in gromos-96 format. Is this possible ?
I understand that I could convert the .xtc file with trjconv. I need
rather high precision, but I am uncertain about the meaning of the
parameter xtc_pr
grivet wrote:
Hi everybody,
In order to use an old set of analysis programs, I would like mdrun to
ouput my trajectory in gromos-96 format. Is this possible ?
No, not directly.
I understand that I could convert the .xtc file with trjconv. I need
rather high precision, but I am uncertain a
On 13/04/2010 12:46 AM, grivet wrote:
Hi everybody,
In order to use an old set of analysis programs, I would like mdrun to
ouput my trajectory in gromos-96 format. Is this possible ?
trjconv will write .g96 format (see trjconv -h), but I don't know if
that is a trajectory format or merely a f
Hello gmx-users
I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic
form or uncharged ends. Neither ffamber or ffopls force fields has a
complete parameter for them. While in ffamber, I have the parameters for
CGLU and NGLU, but not for a Glutamine. Do I need to define it
It's highly unusual to simulate a single amino acid. I don't exactly know
what's your purpose with it, but if you really want to do it, you need to
generate those parameters.
I know there are web services for generating gromos FF parameters for
"unusual" molecules, possibly there are such resources
Chandan Choudhury wrote:
Hello gmx-users
I am trying to simulate an amino acid (say GLN). It can be as a
zwitterionic form or uncharged ends. Neither ffamber or ffopls force
fields has a complete parameter for them. While in ffamber, I have the
This is not true. OPLS can handle isolated
Hi everyone. I'm doing some simulations involving the sugar trehalose, with
the 53a6 force field. There is an odd issue I am having with the rtp file for
trehalose. It seems to be charged. Here is the beginning of the rtp entry:
[ TRH ] [ atoms ] HO4 H 0.41000 0 O4 OA -0
Michael McGovern wrote:
Hi everyone. I'm doing some simulations involving the sugar trehalose,
with the 53a6 force field. There is an odd issue I am having with the
rtp file for trehalose. It seems to be charged. Here is the beginning
of the rtp entry:
[ TRH ]
[ atoms ]
HO4 H
Hello,
while I am running grompp command, I am getting following error.
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 837 of the 2346 non-bonded parameter combinations
---
Program grompp, VERSION 4.0.5
Source cod
Hi,
The sugars were improved in 45a3. The parameters haven't changed for
the later versions.
Cheers,
Tsjerk
On Tue, Apr 13, 2010 at 12:24 AM, Justin A. Lemkul wrote:
>
>
> Michael McGovern wrote:
>>
>> Hi everyone. I'm doing some simulations involving the sugar trehalose,
>> with the 53a6 for
On 13/04/2010 1:49 PM, Jignesh Patel wrote:
Hello,
while I am running grompp command, I am getting following error.
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 837 of the 2346 non-bonded parameter combinations
--
Hi,
I have a slab geometry configuration with water and some ions. I wish to
extract the charge/potential distribution due to ions in the center of my
box. For this I used trajconv to have a box of required dimensions and
center the required ions in it. And then run g_potential on it to get the
ch
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