Dear Mark and Justin,
Hi, Justin, I share the files in the dropbox to you. Thanks.
Here is the output:
tm@tm-HP-Z420-Workstation:~/bmp2$ grompp -f ions.mdp -c pb.pdb -p topol.top -o
ions.tpr
GROMACS:gmx grompp, VERSION 5.0.4
GROMACS is written by:
Emile Apol Rossen Apostolov Herm
Dear Gromacs users,
I was wondering how can I make initial structures for bilayers, micells and
liposomes composed of different lipids including some lipid-like molecules.
I am interested in different mixing ratios in two leaflets in bilayer and
liposome cases.
I have the coordinate and topology
A recent publication by Brown et. al. which appears in the latest issue of
JCTC may also be relevant. See the title below
"Stacking free energies of all DNA and RNA nucleoside pairs and
dinucleoside-monophosphates computed using recently revised AMBER
parameters and compared with experiment "
O
On 4/15/15 10:33 AM, Rebeca García Fandiño wrote:
Dear GROMACS users,
I am trying to concatenate several trajectories
with identical times using the command trjcat with the options -cat and
-settime. I have to introduce manually the option "c" each time a new
trajectory is read. I would like to
On 4/15/15 10:28 AM, soumadwip ghosh wrote:
Dear Tushar,
I dint get what you mean by 'effect of salt
concentration can not be simulated in GROMACS'. I am simulating a single
stranded DNA which is negatively charged in its native state and the added
salt is bound to affect i
On 4/15/15 10:21 AM, Raj D wrote:
Dear Jastin,
Exactly, I would like to study few important mutants which falls well out
of Fe2+ coordinating shell and the study is about to compare dynamics of
the wild type and mutant systems and I hoping a stable simulation with a
crude approximation of acti
I have a script teste.sh which contains:
#!/bin/bash
#$ -S /bin/bash
#PBS -l nodes=8:ppn=6
source /home/dadalt/gmx-5.0.4/bin/
grompp -f md.mdp -c 1UBQ_400_npt.gro -t 1UBQ_400_npt.cpt -p topol.top -o
product.tpr
/usr/lib64/openmpi/bin/mpirun -np 8 mdrun_mpi -v -deffnm product
I use the
Hi Catarina,
I have an MD wrapper that comprises a monitoring mechanism, which allows
terminating a simulation after a certain condition is met. Of course, such
a mechanism interferes with the MD process, but it will usually add just a
bit every so many minutes, checking the results at intervals.
Hi,
Probably not, unless there's lots of people who'd find it useful. You do
have the option of stopping mdrun periodically and scripting a call to gmx
mindist on the final frame to see if a problem was likely to have occurred
over the trajectory. This would be more efficiently performed during th
it's very much similar creating topology for CNT using g_x2top.
You can search mailing list for that. Recently I have published a paper
on fullerene water systems.
http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.998212#.VTKritzF8wA
if you any problem you can contact me.
Thanks
Abhijit
For fullerenes, follow http://www.webcitation.org/66u2xJJ3O and use x2top
to build the topology based on OPLSAA.
Alex
On Wed, Apr 15, 2015 at 12:51 AM, saeed poorasad
wrote:
> Hi Gromacs users ,
> I want to have a system with one C60 and about 1000 water molecules .I
> tried to use pdb2gmx on
Dear Mark,
>>Can't you get the angle you want by subtracting the one you have from 90?
I've tried to solve by add 90, but I found that sometimes it's adding 90,
sometimes it's subtracting, depending on the positions of the two planes?
Xujun
From: gromacs.o
On Wed, Apr 15, 2015 at 7:32 PM, Mirco Wahab
wrote:
> On 15.04.2015 18:41, Andrew DeYoung wrote:
>>
>> Hi,
>>
>> I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was
>> compiled on my system? I would like to know whether the person who
>> compiled Gromacs used gcc or icc (both
Hi,
With version 4.5 extracting the some of information you want is a bit
tricky. Note that starting with GROMACS 4.6 all you need is present in
the "-version" output of any GROMACS tool including compiler
version(s), flags used, options enabled at compilation, etc.
With v4.5 this information is
On 15.04.2015 18:41, Andrew DeYoung wrote:
Hi,
I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was
compiled on my system? I would like to know whether the person who
compiled Gromacs used gcc or icc (both compilers are available and were
presumably available when the compila
Hi,
I'm running Gromacs 4.5.5. Is there a way to determine how Gromacs was
compiled on my system? I would like to know whether the person who
compiled Gromacs used gcc or icc (both compilers are available and were
presumably available when the compilation occurred) and, if possible, what
version
Thank you for the clarification Mark.
Would you consider to add such feature (as an mdrun flag for example: -pi
) in the next GROMACS versions?
On 15 April 2015 at 17:12, Mark Abraham wrote:
> Hi,
> On 15/04/2015 3:55 pm, "Catarina A. Carvalheda dos Santos" <
> c.a.c.dossan...@dundee.ac.uk> wro
Hi,
Can't you get the angle you want by subtracting the one you have from 90?
Mark
On 15/04/2015 5:58 pm, "LIANG Xujun" wrote:
> Dear GROMACS users,
>
> I am now using gromacs 5.0.4 to calculate the angle between the normal
> vector of a plane 1 and the COM (center of mass) vector of plane 1 an
Hi,
On 15/04/2015 3:55 pm, "Catarina A. Carvalheda dos Santos" <
c.a.c.dossan...@dundee.ac.uk> wrote:
>
> Hi there,
>
> Is there any way to control the minimum distance with periodic images
> during mdrun and exit the simulation automatically if this distance is
> equal or lower than the user-defin
Dear GROMACS users,
I am now using gromacs 5.0.4 to calculate the angle between the normal vector
of a plane 1 and the COM (center of mass) vector of plane 1 and plane 2, I used
the following command:
gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 plane 1 (I tried to use
this command
I asked to see the output. You can't be helped without someone seeing that.
Mark
On 15/04/2015 3:12 pm, "Ming Tang" wrote:
> Hi Mark,
>
> pdb2gmx doesn't work, and it reminds the same error. Topol file was simply
> modified by mean from the topol file generated when considering MG2++
>
> Thanks
Dear GROMACS users,
I am trying to concatenate several trajectories
with identical times using the command trjcat with the options -cat and
-settime. I have to introduce manually the option "c" each time a new
trajectory is read. I would like to introduce this line into a script,
in such way I
Dear Tushar,
I dint get what you mean by 'effect of salt
concentration can not be simulated in GROMACS'. I am simulating a single
stranded DNA which is negatively charged in its native state and the added
salt is bound to affect its dynamics. This is of course valid if the force
Hi Prof. David van der Spoel and Dr. Lemkul,
We had quite an interesting discussion related to the entropy calculation
in gromacs-4.5 version.
Lately, I resumed the configurational entropy calculations in the newer
(not latest) version of gromacs.
Presently, I am looking into the results of a pa
Dear Jastin,
Exactly, I would like to study few important mutants which falls well out
of Fe2+ coordinating shell and the study is about to compare dynamics of
the wild type and mutant systems and I hoping a stable simulation with a
crude approximation of active is enough for this purpose because
Hi there,
Is there any way to control the minimum distance with periodic images
during mdrun and exit the simulation automatically if this distance is
equal or lower than the user-defined cutoff? I know that this can be
monitored with g_mindist, but doing it automatically would avoid wasting
simul
On 4/15/15 9:11 AM, Ming Tang wrote:
Hi Mark,
pdb2gmx doesn't work, and it reminds the same error. Topol file was simply
modified by mean from the topol file generated when considering MG2++
We need to see the *actual terminal output* to diagnose this. It would also be
useful if you can
On 4/15/15 8:37 AM, Nataraj Balakrishnan wrote:
Dear Justin,
Thanks for your reply. I just came across one article which uses Fe2+ ion
in the active site and as you mentioned they have used phorpherin structure
to mimic the Fe2+ parameterzation but nothing mentioned explecitily other
parameters
Hi Mark,
pdb2gmx doesn't work, and it reminds the same error. Topol file was simply
modified by mean from the topol file generated when considering MG2++
Thanks
Sent from my Huawei Mobile
Mark Abraham wrote:
Thanks. What is the whole pdb2gmx terminal output?
Mark
On Wed, Apr 15, 2015 at 3:
Hi,
With Gromacs version 5.0.4 I get the same error message as Nizar.
However, with version 4.6.5 everything works fine.
So there may be a bug in the new version.
Kind regards,
Sam
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GM
Dear Justin,
Thanks for your reply. I just came across one article which uses Fe2+ ion
in the active site and as you mentioned they have used phorpherin structure
to mimic the Fe2+ parameterzation but nothing mentioned explecitily other
parameters details. They have used Amber molecular suit for th
On 4/15/15 6:43 AM, Tushar Ranjan Moharana wrote:
Hi Soumadwip,
Did you see any difference at different salt concentrations? I doubt
whether GROMACS can consider salt concentration. Just adding NA and CL
doesn't produce the effect of salt concentration in GROMACS.
If anybody think I am wrong a
On 4/15/15 3:46 AM, Debayan Chakraborty wrote:
As far as I know, AMBER force-fields tend to overestimate the stacking
interactions in nucleic acids, whereas CHARMM tends to understabilize them.
Over all of the ideal stacked base conformations, this is generally true, but
the magnitude of the
On 4/15/15 4:07 AM, rajan kumar wrote:
Dear all,
i am trying to reduce the variation in the h-bond plot in xmgrace. can we
reduce it and how?
Probably what you want is the running average feature (in
Data->Transformations).
-Justin
--
==
Ju
As Justin mentioned in an earlier response you aren't going to be able to use
pdb2gmx for this, instead you are going to need to use x2top if you are going
to build your own topology. Alternatively, you may have better luck building
one by hand (see the gromacs manual, and be prepared to spend a
On 4/15/15 12:19 AM, Raj D wrote:
Dear Users,
Had anybody used Fe2+ ions in the active site of protein. I am planning to
use one using amber99sb forcefield...please suggest to use the nonbonded
parameters for Fe2+ ions, sigma and epsilon values.
Most force field parameters are specifically fo
Thanks. What is the whole pdb2gmx terminal output?
Mark
On Wed, Apr 15, 2015 at 3:05 AM, Ming Tang wrote:
> Dear Justin and mark,
>
> I modified the files like this:
>
> aminoacids.rtp
>
> [ MG ]
> [ atoms ]
> MG MG 2.000
> [ SR ]
> [ atoms ]
> SR SR 2.
On Wed, Apr 15, 2015 at 4:39 AM, Agnieszka Slowicka
wrote:
> >
> >
> > On 4/10/15 12:06 PM, Agnieszka Slowicka wrote:
> >> Hello,
> >> I have a problem with implementation of dihedral restraints in gromacs
> 5.0.4.
> >> I introduced restraints into a topology file after the section with
> protein
Thank you Debayan for your prompt reply. I think now I can conclude that
although classical force fields cannot probe pi-pi stacking directly, the
non-bonded Coulomb and VDW
Soumadwip
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Dear all,
I am using rigid CO2 model with virtual sites. The bond lengthe and LJ
parameters are taken from TraPPE force field (Vapor–liquid equilibria of
mixtures containing alkanes, carbon dioxide, and nitrogen. JJ Potoff, JI
Siepmann. AIChE journal 47 (7), 1676-1682, 2001. 469). I followe
Hi Soumadwip,
Did you see any difference at different salt concentrations? I doubt
whether GROMACS can consider salt concentration. Just adding NA and CL
doesn't produce the effect of salt concentration in GROMACS.
If anybody think I am wrong and effect of salt concentration can be
simulated using
>This isn't mathematically consistent, nor do I think it will be stable. That
>is
>a massive repulsion at just about any distance. For a bit gentler approach,
>please consider what we do with hydrophobic fragments here:
>http://pubs.acs.org/doi/abs/10.1021/ci100462t
Thank you for your advice
Dear all,
i am trying to reduce the variation in the h-bond plot in xmgrace. can we
reduce it and how?
any help will be very appreciated
with best regards
--
*Rajan kumar choudhary*
*Senior Research Fellow*
*Department of Atomic Energy(Govt.Of India)*
*ACTREC TATA Memorial Center *
*Kharghar Na
As far as I know, AMBER force-fields tend to overestimate the stacking
interactions in nucleic acids, whereas CHARMM tends to understabilize them.
The Chen and Garcia paper talks extensively about it (HIgh-resolution
reversible folding of hyperstable RNA tetraloops using molecular dynamics
simulati
The errors mentioned in comment #2 indicates that the system is blowing up
and it is not equilibrated well. It is writing separate step.PDB files
since there are bad contacts. Probably your system is not properly
equilibrated. By the way , i didnot understand what do you mean by 'running
a covalen
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