Dear users,
I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
I¹ve tried to get grompp to work, but I keep getting the following message:
___
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp
And not to forget: most experiments are performed under (more or less)
constant pressure. In that sense, NPT simulations are 'more like the
real thing'.
Cheers,
Tsjerk
On Wed, Feb 18, 2009 at 5:21 AM, chris.ne...@utoronto.ca wrote:
short answer: volume equilibration and therefore density
I read some papers and it seems that more simulation system is under NPT.
What is the benefit for running MD under NPT?
Not every model gives a correct (experimental) density using NPT.
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv
Dean Cuebas wrote:
Dear users,
I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
I¹ve tried to get grompp to work, but I keep getting the following message:
___
creating statusfile for 1 node...
Back Off! I just
dear dean,
there is no problem with your mdp file. for grompp number of atoms in .top
file and input .gro file should be equal,look your.top file, this may be
because u have added number of ions in your .top file but it not present
in your .gro file( difference of 8 atom only in both file, which
Dear gmx-user,
I try to build a pure water box in Gromacs, so I just solved one water as
solute with genbox.
When I use tip3p water, my scripts work well. But to switch to tip4p water,
there seems a bug, I don't know whether people have noticed this or not.
The system shows that it added 350
Dear Justin,
just to answer to your comments: certainly I'm not expecting that things are
going EXACTLY in the same way
every time I repeat them, but it seems quite strange to me that the first time
the system arrives to
convergence and the next time not, with the same parameters...
The other
Hi
I would like to use the gromacs/Gaussian03 interface and i would like to
know if there are any papers with data obtained using this interface.
Thanks a lot
Jacopo
___
gmx-users mailing listgmx-users@gromacs.org
Hi Mark,
I think 3.3.2, does it be fixed in 4.0?
Chao
On Wed, Feb 18, 2009 at 12:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Chao Zhang wrote:
Dear gmx-user,
I try to build a pure water box in Gromacs, so I just solved one water as
solute with genbox.
When I use tip3p water, my
Anna Marabotti wrote:
Dear Justin,
just to answer to your comments: certainly I'm not expecting that things are
going EXACTLY in the same way
every time I repeat them, but it seems quite strange to me that the first time
the system arrives to
convergence and the next time not, with the same
I have played with this recently and could not find the way to set
or change the colors on the volume
slice.
see my previous post about how to do this with black/white and gimp/
photoshop
I did not find any mention of this in your previous post. But it is ok.
Moreover I found that the
Hello,I would like to ask you a (simple) clarification question:Reading the
manual and equations 4.158 up to 4.160 there is a convergence parameter b (with
hellenic letters β).I would like to ask you whether this parameter is the same
as the ewald_rtol that I come accross in the manual. If it
Hello,
I would like to ask you a (simple) clarification question:
Reading the manual and equations 4.158 up to 4.160 there is a convergence
parameter b (with hellenic letters β).
I would like to ask you whether this parameter is the same as the ewald_rtol
that I come accross in the manual. If
Claus Valka wrote:
Hello,
I would like to ask you a (simple) clarification question:
Reading the manual and equations 4.158 up to 4.160 there is a
convergence parameter b (with hellenic letters β).
I would like to ask you whether this parameter is the same as the
ewald_rtol that I come
Chao Zhang wrote:
Hi Mark,
I think 3.3.2, does it be fixed in 4.0?
I don't know - I've not seen it reported. You should search the mailing
list archives.
There won't be any interest in diagnosing or fixing it within version
3.x, but if you can reproduce your result in 4.0.4, file a
On Thu, Feb 19, 2009 at 01:56:28AM +1100, Mark Abraham wrote:
Chao Zhang wrote:
Hi Mark,
I think 3.3.2, does it be fixed in 4.0?
I don't know - I've not seen it reported. You should search the mailing
list archives.
I've solvated with tip4p in 3.3cvs and 3.3.1, never had the problem.
Date: Thu, 19 Feb 2009 01:53:47 +1100
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] ewald_rtol parameter question
Claus Valka wrote:
Hello,
I would like to ask you a (simple) clarification question:
Reading the manual and equations 4.158 up to
Hello list,
does g_mdmat ouput the standard deviation that goes along with the mean.xpm
file? Thank you.
-Rob
_
___
gmx-users mailing listgmx-users@gromacs.org
Dear XAvier,
I have played with this recently and could not find the way to set
or change the colors on the volume
slice.
see my previous post about how to do this with black/white and
gimp/ photoshop
I did not find any mention of this in your previous post. But it is ok.
Sorry for
Hello,
we have built a cluster with nodes that are comprised by the following: dual
core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of
memory. The switch that we use is a dell power connect model. Each node has a
Gigabyte ethernet card.
I tested the performance for
Hello,
I was wondering how to set up parameters for interactions between two
different atoms A and B. Since for Gromacs parameters are defined to each kind
of atom, I cannot specify parameters between A and B. For Buckingham potential,
the rule was:
A_ij=(A_ii * A_jj)^(1/2)
So anyone
Shuangxing Dai wrote:
snip
I also have problem in installing xmgr. I use MacOSX 10.5.5. I type
./configure and got this error messege:
ecme222-96-dhcp:xmgr-4.1.2 ssx$ ./configure
creating cache ./config.cache
checking host system type... configure: error: can not guess host type;
you must
Thanks Berk, 4.0.4 does show the expected behaviour for me with the
twin-range cutoff. Since I obtained 4.0.4 prior to mentioning this
issue, I gather that you gave the free energy code a good looking-over
recently. I really appreciate it.
I have seen only one previous paper that utilized
For LJ interactions, use [ pairtypes ]. For Coulombics there is
unfortunately no analogous solution. I am not clear about exactly what
you want to do. What parameters are you interested in, or by this do
you just mean LJ and Q?
Chris.
-- original message --
Hello,
I was wondering how
Hi,
This was a new issue in 4.0, 3.3 was fine.
Berk
Date: Wed, 18 Feb 2009 13:26:39 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] anomalous free energy dgdl.xvg values every nstlist
steps while using a twin-range cutoff
Thanks Berk, 4.0.4 does
Hi,
No pairtypes are for bonded pair interactions,
not for combinations of non-bonded interactions.
The manual tells you how to do this:
[ nonbond_params ]
A_ii A_jj 2 a b c6
Berk
Date: Wed, 18 Feb 2009 13:31:43 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject:
Hi all,
For those of you using Chimera to work with your Gromacs
trajectories, I just added support for Gromacs 4 .tpr files to
Chimera. This capability is only available in daily builds right
now. You can get a daily build by going to the UCSF Chimera Home Page
and following the Daily
Hello,thank you for your answer. I just wondering though. How am I supposed to
have a system with more than 9 atoms, while the gro file has a fixed format
giving up to 5 digits in the number of atoms?
What else should I change in order to succeed better performance from my
hardware if I
Hi,
Oops, I meant 72000, which is only a factor of 10.
I guess it might be faster one two nodes then, but probably not 2 times.
If you use PME you can also experiment with putting all the PME nodes
on one machine and the non-PME nodes on the other,
probably with mdrun -ddorder pp_pme
Gromacs
*Dear All,
I have compiled fft-3.2.1 in a specific user directory; then configured,
compiled gromacs-4.0.3 from source code according to directions and
installed it in the
specific directory, all without any errors, but at the end make tests
command fails, the output is:
(if test -d gmxtest;
nitu sharma wrote:
*Dear All,
I have compiled fft-3.2.1 in a specific user directory; then configured,
compiled gromacs-4.0.3 from source code according to directions and installed
it in the
specific directory, all without any errors, but at the end make tests
command fails, the output is:
Hello everyone,
I'm gonna run MD simulation with a enzyme/substrate system. Here the
substrate must connected with the side chain of an activity residue of
enzyme through covalent bond. However, i really have no idea about the
preparation of such a complex structure file. Actually, i tried to
Ji Liu wrote:
Hello everyone,
I'm gonna run MD simulation with a enzyme/substrate system. Here the
substrate must connected with the side chain of an activity residue of
enzyme through covalent bond. However, i really have no idea about the
preparation of such a complex structure file.
Dean Cuebas wrote:
Dear users,
I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
I¹ve tried to get grompp to work, but I keep getting the following message:
___
creating statusfile for 1 node...
Back Off!
Dean Cuebas wrote:
Dean Cuebas wrote:
Dear users,
I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
I¹ve tried to get grompp to work, but I keep getting the following message:
___
creating statusfile for 1 node...
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
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