Hi,
The triclinic representation is used for all boxes in Gromacs as it is the
most compact. One needs to invoke trjconv with -pbc mol -ur compact to
obtain the expected visualization.
Well, it's not the most compact (otherwise -ur compact would yield you
a brick again), but it's the
Hi Fabian,
The tpi integrator will caluclate it for you when you simply add the extra
molecule to your gro and topology:
http://www.mail-archive.com/gmx-users@gromacs.org/msg50610.html
Best,
Jan
From: gmx-users-boun...@gromacs.org
Dear Users,
I am trying to analyze a ligand-protein simulation results. I read in the
manual that using g_rms command with –bm option produces a matrix of average
bond angle deviations. And only bonds between atoms in the comparison groups
are considered. Does it mean that it is for the bonds
Dear all,
would it be possible to send me the necessary files in order to start the
Gromacs simulations of thin film of SiO_2 (preferably amorphous)?
Do people use Gromacs force fields for this, or BKS potential?
Thanks a lot in advance,
Yours, alexey
I increased the potential to 2350 instead of 1000 in my md_umbrella.mdp (the
other parameters kept unchanged), then the movement of my protein was less than
the previous one, which we can see from pullx.xvg (attached). But it still not
reach to the designed region. So I am going to increase
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
Cheers,
Alan
On 22 May 2012 12:36, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/22/12 12:46 PM, Alan wrote:
Hi Justin, your suggestion got close. However, let me give an
On 23/05/2012 6:42 PM, Alan wrote:
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
One useful approach is to simplify the system as much as possible before
producing the .tpr and using gmxdump. The necessary
Dear Alexey,
The answer to this question partly depends on your application- for example,
is it important for the surface of the amorphous SiO2 to be able to undergo
reactions like Si-O-Si + H2O = 2SiOH?
Regards,
Jim Rustad
--
View this message in context:
Hallo together,
in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or pose them.
Thanks a lot
Sebastian
--
gmx-users mailing listgmx-users@gromacs.org
hi Jim,
first of all, thanks for the answer.
No, for me it is not important. Our task is to simulate natural rubber
between two silica surfaces, i.e, no water will be present.
Do you have some initial files?
thanks, alexey
*
Dr. Alexey V. Lyulin
Alexey
I have a quartz(101) surface and a gromacs BKS input file that might get you
started at least.
Cheers
Jim
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View this message in context:
http://gromacs.5086.n6.nabble.com/Gromacs-files-to-simulate-SiO2-film-tp4997666p4997673.html
Sent from the GROMACS Users Forum mailing list archive at
i am stimulting an AMP protein in water.
this is the error i get on my first step..
pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce
error:
Fatal error: atom C not found in buiding block 19NH2 while combining
tdb and rtp
please HELP!!
--
gmx-users mailing list
On 5/23/12 12:17 PM, SebastianWaltz wrote:
Hallo together,
in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or pose them.
There is no H3 in NPRO. It is a
On 5/23/12 1:26 PM, ankita oindrila wrote:
i am stimulting an AMP protein in water.
this is the error i get on my first step..
pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce
error:
Fatal error: atom C not found in buiding block 19NH2 while combining
tdb and rtp
please HELP!!
The picture of pullx.xvg is not really helpful. The reason is that in
pullx.xvg the second column (after the time) is the position of the
reference group (which naturally moves; but it's not the thing in which
wie are interested) and the third column is the distance from the
reference group to
Dear GMX-users,
I am trying to use g_polystat in order to calculate persistence length of
DNA oligomer, 60bp. From g_polystat -h I understood that this function
provides the persistence length measures in number of bonds between
consequtive atoms making DNA backbone. Using this function I obtain
Thank you Jan.
-Fabian
On Tue, May 22, 2012 at 6:54 PM, Fabian Casteblanco
fabian.castebla...@gmail.com wrote:
Hello community,
I'm just trying to explore what kind of calculations one can do on
polymer systems (pure or in water) in order to validate the force
field works accurately for
Hi Patrick,
There is a fast decay of the hbond acf for liquid water on a 100-200 fs
timescale that traditionally is associated with the librational motion of water
molecules. There's a good paper by Omer Markovich and Noam Agmon in J. Chem.
Phys. 129 084505 2008 where this effect is discussed,
Hi Gromacs Friends,
I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl script
1. After command perl distances.pl I got following
Dear Thomas,
I just finished the run of 2ft with potential 3000. It is much better than
previous ones. But it still has 1 nm fluctuation along z-axis. I am going to
increase potential to 5000, crazy :)
For the pullx.xvg, I mistaken the second column as the COM position of pulled
group, the
://lists.gromacs.org/pipermail/gmx-users/attachments/20120523/3cbd7a8f/attachment.html
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On 05/23/2012 02:16 PM, Justin A. Lemkul wrote:
On 5/23/12 12:17 PM, SebastianWaltz wrote:
Hallo together,
in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if someone could add the missing parameters or
On Wed, May 23, 2012 at 7:30 PM, Du Jiangfeng (BIOCH)
j...@maastrichtuniversity.nl wrote:
For your second problem: you have to create this file by writing the group
numbers, which inform the script to decide which two groups
Thank you... Du Jiangfeng
Yes problem get solve!!!
Thank you
All
Thanks much for your previous help. I now have the calculation running.
However I get suspicious results that make me think that BAR may not be
integrated with tables correctly.
In this problem I am trying to change an Mg ion into an Fe ion (really its a
ferrous iron to a ferric iron, but
Hallo,
I have several (12) simulations running in which I simulate a protein
in a water box (cubic 9x9x9). For all simulations I can see the
following:
After a few simulations (total time of 7.6ns) the protein moves out of
the water box - for all the twelve simulations. Since the following
On 5/23/12 3:48 PM, rama david wrote:
Hi Gromacs Friends,
I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl
On 5/23/12 4:08 PM, SebastianWaltz wrote:
On 05/23/2012 02:16 PM, Justin A. Lemkul wrote:
On 5/23/12 12:17 PM, SebastianWaltz wrote:
Hallo together,
in the amino acid data base file (aminoacids.rtp) of the amber99sb-ildn
force field the H3 hydrogen of NPRO is missing.
Would be nice if
Hi everybody,
I am installing Gromacs, in the shell it is said that Gromacs has been
installed :
GROMACS is installed under /home/Program/gromacs-4.5.
but I couldn't find the directory bin under /gromacs-4.5, I don't know I have
installed successfully or not, any one could help?
There are a few possibilities.
1. Numbering in [distance_restraints] is not based on .gro numbering. The
atom
numbers supplied are only relevant within the [moleculetype] to which they
belong, much like [position_restraints]. Also make sure that the
[distance_restraints] block is in
On 5/23/12 8:26 PM, tdgrant1 wrote:
There are a few possibilities.
1. Numbering in [distance_restraints] is not based on .gro numbering. The
atom
numbers supplied are only relevant within the [moleculetype] to which they
belong, much like [position_restraints]. Also make sure that the
On 5/23/12 7:55 PM, aiqunhu...@knights.ucf.edu wrote:
Hi everybody,
I am installing Gromacs, in the shell it is said that Gromacs has been
installed :
GROMACS is installed under /home/Program/gromacs-4.5.
but I couldn't find the directory bin under /gromacs-4.5, I don't know I have
On 5/23/12 9:37 PM, aiqunhu...@knights.ucf.edu wrote:
Hi Justin, thanks a lot for replying.
Regarding your question, in the beginning there were errors like this in
config.log:
cc: error: unrecognized option '-V'
cc: fatal error: no input files
compilation terminated.
configure:4343: $? = 4
Dear Gromacs users,
I have question about restarts
First I did 50 ns (time step 2fs, total steps 25*10^6) run for my system.
Then to extend the run to another 50 ns, I used the following method, :
tpbconv_dp -s equil_01.tpr -nsteps 5000 -o equil_02.tpr
Since I am doing a mutation study, I
On 5/23/12 10:06 PM, aiqunhu...@knights.ucf.edu wrote:
Hi Justin,
I am gonna reinstall Gromacs 4.5.5, and this time I am not gonna use LAM or MPI.
But can you explicitly tell me what inconsistencies are in my commands?
Please ignore that earlier remark. I misread your directory structure
On 5/23/12 10:26 PM, Shyno Mathew wrote:
Dear Gromacs users,
I have question about restarts
First I did 50 ns (time step 2fs, total steps 25*10^6) run for my system. Then
to extend the run to another 50 ns, I used the following method, :
tpbconv_dp -s equil_01.tpr -nsteps 5000 -o
Dear all gromacs users,
while running the command grompp -c
1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp i am getting the
following error.
File input/output error:
pr.mdp
Dear all gromacs users,
I am new for MD and in particular using
gromacs software.I would like to learn basics of gromacs.Please tell me the
name of the manual which one is suitable for me.
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
--
gmx-users
Thank you justin..
I solve script problem..
I have another query ..
As mention in tutorial , In step six , we have to do brief NPT
equilibration
npt_umbrella.mdp link is
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
After these we have
On Thu, May 24, 2012 at 10:39 AM, Seera Suryanarayana
paluso...@gmail.comwrote:
Dear all gromacs users,
I am new for MD and in particular using
gromacs software.I would like to learn basics of gromacs.Please tell me the
name of the manual which one is
On Thu, May 24, 2012 at 10:20 AM, Seera Suryanarayana
paluso...@gmail.comwrote:
Dear all gromacs users,
while running the command grompp -c
1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp i am getting the
following error.
On 5/24/12 7:11 AM, rama david wrote:
Thank you justin..
I solve script problem..
I have another query ..
As mention in tutorial , In step six , we have to do brief NPT equilibration
npt_umbrella.mdp link is
Dear Users,
I am trying to analyze a ligand-protein simulation results. I read in the
manual that using g_rms command with –bm option produces a matrix of average
bond angle deviations. And only bonds between atoms in the comparison groups
are considered. Does it mean that it is for the
On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote:
Dear Users,
I am trying to analyze a ligand-protein simulation results. I read in the manual
that using g_rms command with –bm option produces a matrix of average bond angle
deviations. And only bonds between atoms in the comparison groups are
Hi Justin,
Thank you for your Reply
Before start tutorial I read your paper, It help me
a lot to understand the concept of umbrella sampling...
But truly I not understand the part in six step
why to use define -DPOSRES_B and not -DPOSRES,
I think I miss it ...
I will be a very greatfull to
On 5/24/12 7:40 AM, rama david wrote:
Hi Justin,
Thank you for your Reply
Before start tutorial I read your paper, It help me
a lot to understand the concept of umbrella sampling...
But truly I not understand the part in six step
why to use define -DPOSRES_B and not -DPOSRES,
I think I
Hi,
I tried protein protein simulation in gromacs.
I prepared one ptn and kept seperately with its .top, .itp, .gro files.
Then I prepared another protein and I build the complex of pasting the .gro
file of first processed protein in the .gro file of second processed ptn.
In the topol.top of
Hi all,
I am using tabulated potential option for non bonded
interactions. The system that i am using contains on CA(alpha) CB(beta)
,atoms connected, If i use option
energygrps = CA CB
energytable = CA CA CB CB it caluclates potential
between
On 5/24/12 7:43 AM, rethina malliga wrote:
Hi,
I tried protein protein simulation in gromacs.
I prepared one ptn and kept seperately with its .top, .itp, .gro files.
Then I prepared another protein and I build the complex of pasting the .gro file
of first processed protein in the .gro file
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