hi,
i am pasting the xmgrace file for the both forward and reverse
transformation of charge modification for Ala->Gly mutation.
The simulations are performed in water. when you open the file with
xmgrace, you can clearly see the behaviour what i was describing in
previous mails.
bharat
it seems there's a problem with my compiler. I succesfully run grompp
in another computer with
gromacs distribution. I compare and check the two ggc version.
On Nov 9, 2007 7:10 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> > I installed ffamber ports for gromacs, generated gro and topology
> >
> I installed ffamber ports for gromacs, generated gro and topology
> files for a DNA structure with pdb2gmx, a box with editconf and added
> solvation with genbox. When I try to run grompp i obtain these errors:
>
>
> checking input for internal consistency...
> calling cpp -traditional...
> proce
> Dear gromacs users,
>
>
>
> I am trying to set up a system with new (non-standard) residue blocks to
> study polymers and polymer-protein conjugates; however we will not have
> pdb
> files of molecules that we want to study.
Jumping straight in the deep end is a recipe for frustration. Make sure
I installed ffamber ports for gromacs, generated gro and topology
files for a DNA structure with pdb2gmx, a box with editconf and added
solvation with genbox. When I try to run grompp i obtain these errors:
checking input for internal consistency...
calling cpp -traditional...
processing topology
>
> hi i am trying to run mdrun for protein in membrane system. When i run
> mdrun i get a warning
Check out the wiki link Justin provided. Also read
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and make
sure your setup regime is reasonable.
Also, when you run grompp, pay atten
> I want to use replica exchange method. After obtaining all files at
> different temperatures, how can I load the e.g 4 separate replica files to
> the mdrun command?
> I could not find any information about it.
See mdrun -h.
Please choose a meaningful subject for your emails.
Mark
___
DIY on the admin panel
http://www.gromacs.org/index.php?option=com_wrapper&Itemid=83
On 11/9/2007 11:04 PM, Henry O Ify wrote:
Hell my friend, i dont need any of this messages from all the members
of this board, please help alert the board, its bored reading them
all, i want to unsubscribe fro
I want to use replica exchange method. After obtaining all files at different
temperatures, how can I load the e.g 4 separate replica files to the mdrun
command?
I could not find any information about it.
Thank you
Oz.
___
gmx-users mailing listg
Hell my friend, i dont need any of this messages from all the members of this
board, please help alert the board, its bored reading them all, i want to
unsubscribe from the group
Yang Ye <[EMAIL PROTECTED]> wrote: it could not be possible since amber force
field doesn't parameterized
NLYN. al
this is a too general question. please read the wiki first.
On 11/9/2007 9:58 PM, Kitty Ji wrote:
> Dear users:
> After we get some data from GMX simulation, how can we validate them?
> I met many difficulties in parameters setting.
> ___
> Kitty JI
> Groupe
Dear users:
After we get some data from GMX simulation, how can we validate them?
I met many difficulties in parameters setting.
___
Kitty JI
Groupe Matière Condensée et Matériaux
UMR-CNRS 6626
Bat. 11A, Campus de Beaulieu
Université de Rennes 1
35042 Renne
On 11/9/2007 9:21 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 9:09 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds li
ACE for the N-termail and NME for the C-terminal. They are neutral. You
can do so with aids from PyMol...
Regards,
Yang Ye
On 11/9/2007 9:50 PM, Hu Zhongqiao wrote:
Thanks, Yang Ye.
You mean that I put an additional ACE or NME on the N-terminal lysine
residue?
zhongqiao
Message: 3
Date
Check out the wiki at:
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
Alternatively, search the list for some of my posts from around a year ago - NVT
and minimization of a lipid bilayer (or search for my name, they should come up
as well). I suspect you have bad contacts in your starti
Thanks, Yang Ye.
You mean that I put an additional ACE or NME on the N-terminal lysine
residue?
zhongqiao
> Message: 3
> Date: Fri, 09 Nov 2007 20:03:21 +0800
> From: Yang Ye <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1
> unitcharge?
> To:
hi i am trying to run mdrun for protein in membrane system. When i run mdrun i
get a warning
Step -2, time -0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 2.144082 (between atoms 12433 and 12434) rms 0.216090
bonds that rotated more than 30 degrees:
atom 1 atom 2 angl
Yang Ye wrote:
On 11/9/2007 9:09 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 an
On 11/9/2007 9:09 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU 7.1
Yang Ye wrote:
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new.
Herein I just suggest and
pragya chohan wrote:
> Date: Thu, 8 Nov 2007 12:35:29 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] installation
error>> pragya chohan wrote:>> hi>> I had installed make_hole utility earlier but when i tried to run:>>
> Date: Thu, 8 Nov 2007 12:35:29 +1100>
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users]
installation error>> pragya chohan wrote:>> hi>> I had installed make_hole
utility earlier but when i tried to run:>> make_hole.pl -f box_
Dear gromacs users,
I am trying to set up a system with new (non-standard) residue blocks to
study polymers and polymer-protein conjugates; however we will not have pdb
files of molecules that we want to study.
Is there a way of generating coordinate files and other necessary Gromacs
fil
Hi,
Please be clear that failed test: simple/rb1 and complex/acetonitrilRF
are due to different reasons. So far, simple/rb1 remains unknown but
complex/acetonitrilRF has been solved. Also, a segmentation fault is
different from results having difference to the benchmark data. Please
be exact
Yes. Mine is 32-bit. Intel P4 3.0G.
On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote:
> Dear Li Qiang,
>
> >> it seems another guy get the same error(cannot pass gmxtest with
> >> rb1/acetonitrilRF) as me. and it sounds like the compatible problem
> >> between GROMACS 3.3.2 and and UBUNTU 7.
I see. thanks for the information.
but one of my friends nearby failed on this combination just few hours
ago. Maybe we need more test for the conclusion.
Li Qiang
On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote:
> Dear Li Qiang,
>
> >> it seems another guy get the same error(cannot pass gm
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new.
Herein I just suggest and hope others may
it could not be possible since amber force field doesn't parameterized
NLYN. alternative, use ACE/NME to cap the peptide.
On 11/9/2007 7:36 PM, Hu Zhongqiao wrote:
Hi,
I am using amber force field in Gromacs. The protein I simulated is
the lysozyme (PDBID: 1HEL). I want to set all lysine
> Dmytro Kovalskyy wrote:
>> Hi there,
>>
>> Gromacs explodes with new version of libc
>
> Did you compile it yourself?
> Could you please recompile it with
> CFLAGS=-g
> and try to debug it?
>
> Which OS and compilers did tou use?
The story does not end here.
I found that behavior of GROMACS dep
Hi,
I am using amber force field in Gromacs. The protein I simulated is the
lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral.
According to rules using Amber in Gromacs, neutral lysine should be
named to LYN. Everything goes smoothly except the N-terminal lysine
residue. I
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new.
Herein I just suggest and hope others may help to install 3.3.2 on new
ubuntu 7.10
From: "Frankie Montenegro" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: Re: [gmx-users] bonded Buckingham interaction
Date: Fri, 9 Nov 2007 04:47:02 -0500
Well, that's not an option, I am using a modified Morse interaction
Frankie Montenegro wrote:
Well, that's not an option, I am using a modified Morse interaction
already. That
was straightforward, I only needed to modify bondfree.c
But I saw in the manual (after sending the first email) the list of
files that need to be modified to add a bonded interaction, so I'
Well, that's not an option, I am using a modified Morse interaction
already. That
was straightforward, I only needed to modify bondfree.c
But I saw in the manual (after sending the first email) the list of
files that need to be modified to add a bonded interaction, so I'll
try that. BTW, it would b
Frankie Montenegro wrote:
Hi everyone,
I am trying to implement a force field for a metalorganic crystal. In this FF,
there is a Buckingham interaction between two neighboring atoms, O and Zn.
This interaction exists only for atoms on the same crystal site.
How about using a Morse potential? I
Hi everyone,
I am trying to implement a force field for a metalorganic crystal. In this FF,
there is a Buckingham interaction between two neighboring atoms, O and Zn.
This interaction exists only for atoms on the same crystal site.
So, bonded Buckingham interaction added in [ pairs ] would be a
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