Hi,
I just fixed this in 4.0.4.
The forces are always correct, dgdl in 4.0.3 was only correct at nstlist steps.
Currently 4.0.4 is only available through ftp.
We still need to add it (and the release notes) to the download page.
Berk
> Date: Tue, 17 Feb 2009 17:50:17 -0500
> From: chris.ne...@
short answer: volume equilibration and therefore density
equilibration. Even people who do constant volume production
simulations usually do an initial constant pressure simulation to get
the density correct.
better answer: find a good simulation textbook and give it a read.
Allen and Til
HI
I read some papers and it seems that more simulation system is under NPT.
What is the benefit for running MD under NPT?
Thank you
Lin
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gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search
Peggy Yao wrote:
Dear all,
I am trying to use amber03 force field. I corrected the amino acid names
as described on http://chemistry.csulb.edu/ffamber/.
However, when I ran pdb2gmx on a PDB file without H-atoms, I got the
following error:
pdb2gmx -ff amber03 -f protein_without_H.pdb -o p
Dear all,
I am trying to use amber03 force field. I corrected the amino acid names as
described on http://chemistry.csulb.edu/ffamber/.
However, when I ran pdb2gmx on a PDB file without H-atoms, I got the
following error:
pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb
...
W
Download charmm and run it to make your .psf. There are some examples on the
charmm forum.
If you have further problems, you would be better to post to the charmm forum:
http://165.112.184.13/ubbthreads/ubbthreads.php?Cat=
If you need to make a .psf and only have a .gro, then use "editconf -f a.
Dear all,
I am trying to make .psf file based on .gro or .pdb file with
information of atom bonds which is arbitrarily defined.
Could someone give me how to make .psf file?
(Should I make a original program for making .psf file?)
Thanks,
Hideya Nakamura
hideyanakam...@gmail.com
Peggy Yao wrote:
Dear all,
I'd like to study intra-molecular hydrogen bonding. Which force field
would you recommend?
I have been working on G43a1 and OPLS. OPLS seems quite good. It places
all H-atoms. However, G43a1 only considers H-atoms on N-atoms, but not
C-atoms. Even if I input a f
Peggy Yao wrote:
Thank you, Justin.
I am using GMX 4.0.2. Do I need to have the -np option in all grompp and
mdrun commands? Thanks in advance!
Read the -h of each program, as well as the numerous threads on the topic in the
list archive.
-Justin
Peggy
On Tue, Feb 17, 2009 at 3:02 P
Thank you, Justin.
I am using GMX 4.0.2. Do I need to have the -np option in all grompp and
mdrun commands? Thanks in advance!
Peggy
On Tue, Feb 17, 2009 at 3:02 PM, Justin A. Lemkul wrote:
>
>
> Peggy Yao wrote:
>
>> Dear all,
>>
>> In order to run Gromacs on multiple processors, I should put
Dear all,
I'd like to study intra-molecular hydrogen bonding. Which force field would
you recommend?
I have been working on G43a1 and OPLS. OPLS seems quite good. It places all
H-atoms. However, G43a1 only considers H-atoms on N-atoms, but not C-atoms.
Even if I input a fully-added-H-atom PDB fil
The _d denotes that the command is the double precision version.
Command does exactly the same things, just at double precision which
may or may not make any difference to the result.
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 18
Hi Peggy:
the difference between comand an comand_d is that comand is with gromacs
compile in single precision and comand_d the program is compile in
double precision. cheers,
pedro
On Tue, 2009-02-17 at 14:56 -0800, Peggy Yao wrote:
> Dear all,
>
> In the manual, almost all commands have 2 versi
Peggy Yao wrote:
Dear all,
In order to run Gromacs on multiple processors, I should put the number
of processors in the commands. For example,
grompp -np -o topol.tpr
Only if you're using GMX < 4.0.
My question is: nr should be the number of processors, or the number of
cores? If I
Peggy Yao wrote:
Dear all,
In the manual, almost all commands have 2 versions: command and
command_d. For example, pdb2gmx, and pdb2gmx_d. What is the difference?
I searched in both the manual and the internet, but was not able to find
the answer.
You can check by using both the single-
Dear all,
In order to run Gromacs on multiple processors, I should put the number of
processors in the commands. For example,
grompp -np -o topol.tpr
My question is: nr should be the number of processors, or the number of
cores? If I have a quad-core processor, should I put 4?
Thanks,
Peggy
Dear all,
In the manual, almost all commands have 2 versions: command and command_d.
For example, pdb2gmx, and pdb2gmx_d. What is the difference? I searched in
both the manual and the internet, but was not able to find the answer.
Thanks!
Peggy
___
gmx
Hello,
I believe that the free-energy code dgdl contribution from the
twin-range cutoff is being calculated incorrectly in gromacs 4.0.3 (and
probably other versions as well).
Specifically, I notice that the dgdl values spike at nstlist intervals.
This can be seen directly from my dgdl.xvg a
Berk that would be handy. Option in that, could you may be have not to
change the name at all and use the names specified on the command line?
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 17/02/2009, at 6:01 PM, "Berk Hess" wrote:
Ricardo Tosta wrote:
Hi there!!
I'm having trouble installing the Gromacs 4.0.3 on SGI Altix Itanium.
I stopped at the ./configure --enable-mpi command then it gives the error:
checking build system type... ia64-unknown-linux-gnu
checking host system type... ia64-unknown-linux-gnu
checking fo
Hi there!!
I'm having trouble installing the Gromacs 4.0.3 on SGI Altix Itanium.
I stopped at the ./configure --enable-mpi command then it gives the error:
checking build system type... ia64-unknown-linux-gnu
checking host system type... ia64-unknown-linux-gnu
checking for a BSD-compatible instal
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
"Moreover I found that the
colors, although clearly showing the
expected pattern for th
Dear Jinyao,
this is quickly becoming a vmd-mailing list question, but I'll give it
one more set of replies. I would appreciate if you would coallate these
into a single how-to and put it on the gromacs wiki once you have
figured out how to do it.
>Dear chris,
> Thank you for you help.
> I
Ragnarok sdf wrote:
I have tried with decane, octane and CCl4. The three of them got me
the same problem, pressure scaling more than 1%. I have tried
increasing the tau_p value, cause that was one of the solutions given
in gmx user's list. That didn´t work out either. All my simulations
were ca
Justin A. Lemkul wrote:
Bad idea, if the minimization didn't converge.
I should amend that: "Bad idea, if the minimization didn't converge to
reasonable values of Epot and Fmax."
-Justin
Step 502, time 1.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 25670116.0
I have tried with decane, octane and CCl4. The three of them got me
the same problem, pressure scaling more than 1%. I have tried
increasing the tau_p value, cause that was one of the solutions given
in gmx user's list. That didn´t work out either. All my simulations
were carried out using ffgmx fo
Anna Marabotti wrote:
Dear Justin,
I would like to say that now all things work...but it isn't!
I tried to minimize my system with emtol 500 and emstep 0.1, then 0.5, then
with emtol 1000 and emstep 0.5 and
1, but this time I did not arrive to convergence. It seems to me that every
time I us
Hi,
This is just a maintenance release - with fixes for a bunch of minor
things that have been reported on bugzilla. Find it in the usual place:
ftp://ftp.gromacs.org:/pub/gromacs/gromacs-4.0.4.tar.gz
Cheers,
Erik
PS: We haven't forgotten those of you that like binaries, but we're
rework
Dear Justin,
I would like to say that now all things work...but it isn't!
I tried to minimize my system with emtol 500 and emstep 0.1, then 0.5, then
with emtol 1000 and emstep 0.5 and
1, but this time I did not arrive to convergence. It seems to me that every
time I use this system, it
"behaves
>Hello, I would like to know if there is any recommendation onto
>setting up a system with a protein in a apolar solvent box. If there
>is any tutorial or web page with topologies for solvents. I read that
>the decane box that comes with gromacs is not to be used for
>simulations, if that is true,
Greetings
I am working witha system that has two heptadecanol lattices oriented toward
each other with a slab of water between. The alcohol uses the OPLS-AA
parameters and the water is NE6 (Nada and Eerden six-site model). When I
ran the system with the alcohols positionally fixed and their inter
Anna Marabotti wrote:
Dear Justin,
I hope you wouldn't mind if I contact you directly, but I think I cannot send
you the requested .log file via
the gmx-users list because the message would be filtered.
It is best to keep the discussion on the list; posting short .mdp files (pasted
into the
Rebeca García Fandiño wrote:
Hello,
I am trying to do Replica Exchange with 50 replicas, but I am having
problems when using trjcat with -demux.
trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc
mdA_6.xtc mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc
md
Hello,
I am trying to do Replica Exchange with 50 replicas, but I am having problems
when using trjcat with -demux.
trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc mdA_6.xtc
mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc mdA_13.xtc
mdA_14.xtc mdA_15.xtc m
Hello,
I am trying to do Replica Exchange with 50 replicas, but I am having problems
when using trjcat with -demux.
trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc mdA_6.xtc
mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc mdA_13.xtc
mdA_14.xtc mdA_15.xtc m
Anna Marabotti wrote:
Dear Justin,
many thanks for your answer. The removal of problematic water was just a
"desperate" trial I made to find a
solution to this problem. During my attempts, I changed:
- the box size (for this particular system, I use a cubic box of 0.9 nm per
side: I enlarged
Dear Justin,
many thanks for your answer. The removal of problematic water was just a
"desperate" trial I made to find a
solution to this problem. During my attempts, I changed:
- the box size (for this particular system, I use a cubic box of 0.9 nm per
side: I enlarged it until 1 nm,
but nothin
Ragnarok sdf wrote:
Hello, I would like to know if there is any recommendation onto
setting up a system with a protein in a apolar solvent box. If there
is any tutorial or web page with topologies for solvents. I read that
the decane box that comes with gromacs is not to be used for
simulations
Hello, I would like to know if there is any recommendation onto
setting up a system with a protein in a apolar solvent box. If there
is any tutorial or web page with topologies for solvents. I read that
the decane box that comes with gromacs is not to be used for
simulations, if that is true, then
Hi,
Sorry, I don't have time to help you with that.
This is a mailing list for helping people with the use of Gromacs,
not for helping people develop there own code.
Berk
> Date: Tue, 17 Feb 2009 21:02:32 +0800
> From: x...@home.ipe.ac.cn
> To: gmx-users@gromacs.org
> Subject: [gmx-users] RE: R
Hi, Berk
Thank you for your explain!
I have a little parallel program about simulating long chain molecules.
Because of the difficulties in parallel, the atoms of the chain molecules
are stored in the space grid. That is to say first I use domain decomposition
to split the whole simulation spac
Anna Marabotti wrote:
I'm resending the message without attachments, since the previous one was
filtered because it was too big.
Please let me know how to send infos without being filtered, if more
information are needed to help me. I
tried again and again, changing settings and options for m
Srinivasan Ramachandran wrote:
Hi,
Can anyone help with the error we are getting while running this tutorial.
command is
grompp –f em.mdp –c trp_b4em.pdb –p trp.top –o em.tpr
error is
Number of coordinates in coordinate file (trp_b4em.pdb, 28381) does not
match with topology file(trp.top, 28
I'm resending the message without attachments, since the previous one was
filtered because it was too big.
Please let me know how to send infos without being filtered, if more
information are needed to help me. I
tried again and again, changing settings and options for minimization, but I
had no
Hi,
Can anyone help with the error we are getting while running this tutorial.
command is
grompp –f em.mdp –c trp_b4em.pdb –p trp.top –o em.tpr
error is
Number of coordinates in coordinate file (trp_b4em.pdb, 28381) does not
match with topology file(trp.top, 28397)
We follow as per the guide but
ch, CA 90840-9401
> Office/Lab: MLSC-233/MLSC-300
> Phone: 562.985.7537
> Email: eso...@csulb.edu
> Web: http://chemistry.csulb.edu/esorin/
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1. My solute molecule is planar molecule. When I load my *.cube
file to VMD, the solute molecule is not perpendicular to any axis.
your question is not clear! You may reorient your solute prior giving
it to VMD.
Some gmx tools allow to do this. you could fit to a reference
structure that i
Hi,
I would help a lot if you would tell us what you are trying to accomplish.
When charge groups move from one node to an other, only
the global charge group index is communicated (and of course
x and v of the atoms in the cg). Since every node knows
the global topology it can figure out all th
Dear chris,
Thank you for you help.
I have solved my problem. If I use VMD at XP system,the volumeslice is
displayed.
I am apologized it that I still have some difficulties to bother you.
1. My solute molecule is planar molecule. When I load my *.cube file to VMD,
the solute molecule is no
Fellow GROMACS users,
In answer to the many messages we've received regarding ffAMBER ports for
GROMACS 4.0, we've recently posted validated AMBER ports for versions 4.0.2 and
4.0.3 (http://chemistry.csulb.edu/ffamber/). I hope you find them useful!
Also, we're working on several future additi
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