Hello Momin
The best tool I have found for dealing with cif files, including exporting
to pdb, is Mercury. You can download it for free from:
https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/
Hope this helps
Victor
El mar., 13 nov. 2018 a las 8:04, Momin Ahmad ()
escribió:
> Hi,
the extra bonds you observe could be an artifact of the visualizer. Most
molecular visualizers determine where to put bonds by a simple maximum
distance criterion. It may be that your molecules are distorted so that
some atoms are so close that the visualizer thinks there is a bond.
Hope this h
El jue., 23 ago. 2018 a las 17:03, Mark Abraham ()
escribió:
> Hi,
>
> [snip, snip]
> Despite this, there are times when one might want to use such an algorithm,
> and so we permit users to suppress warnings from grompp with -maxwarn.
> However, encouraging such behaviour leads to people abusing
try "-pbc whole" instead of "-pbc mol"
El sáb., 7 jul. 2018 a las 2:13, Anjana Jayasinghe ()
escribió:
> Dear All,
> In my simulation, part of my molecule is in a one cell and the other part
> is in the adjacent cell. I want to get the complete molecule in the pdb
> format in the center of the bo
You can type your abstract in these services:
https://journalsuggester.springer.com/
https://journalfinder.elsevier.com/
https://www.edanzediting.com/journal-selector
and they will give you lists of journals that publish papers similar to
yours.
Hope this helps
Victor
2018-04-20 9:36 GMT-05:
rs-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Victor
> Rosas Garcia
> Sent: 16 November 2017 16:01:23
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] tabulated pair interactions file format
>
> make sure that yo
make sure that your table is named "tablep.xvg" and it is accesible in the
working directory.
Victor
2017-11-16 3:29 GMT-06:00 Srinivasa Ramisetti :
> Dear Gromacs users,
>
>
> I am trying to simulate a single molecule of undecanoic acid using a
> tabulated LJ6-12 potential, but I am getting err
You could try resizing the box of your system with gmx editconf, so the box
does not include the region below the bilayer, add solvent with either gmx
insert-molecules or gmx solvate, and then use gmx editconf again to leave
the box as it was before adding the solvent.
Hope this helps
Victor
20
Wow. My first bug uncovered in GROMACS.
Thanks.
Victor
2017-02-09 0:16 GMT-06:00 David van der Spoel :
> On 08/02/17 23:48, Victor Rosas Garcia wrote:
>
>> Hello everybody,
>>
>> I am having problems with gmx solvate. I am trying to solvate a small
>> peptide wit
Hello everybody,
I am having problems with gmx solvate. I am trying to solvate a small
peptide with a solvent shell 1.2 nm thick. When I use the following
command line:
gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
../topol.top
I get the following message:
OK, thanks.
2016-12-08 10:57 GMT-06:00 Mark Abraham :
> Hi,
>
> I literally have no idea, but I have heard from Szilard Pall that it can be
> done and runs reasonably :-)
>
> Mark
>
> On Fri, Dec 9, 2016 at 3:49 AM Victor Rosas Garcia >
> wrote:
>
> > In
Interesting.
Mark, would you mind pointing out a few resources on how to configure for a
Gigabit network? So far I have found J Comput Chem 28: 2075–2084, 2007, but
there must be something else out there.
Victor
2016-12-08 10:08 GMT-06:00 Mark Abraham :
> Hi,
>
> Thanks for the tip. I would fur
You just did.
Victor
2016-11-24 14:51 GMT-06:00 Sanim Rahman :
> Hello,
>
> I would like access to post to the mailing list. Thank you!
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Undergra
I thought the "build" directory had to be *outside* the gromacs source
directory. Don't know for sure if that makes a difference.
2016-08-18 18:20 GMT-05:00 Quentin Kaas :
> Hi Mark,
>
> Thank you for your answer. I just have redone again everything but I get
> the same problem. I am not even co
The following paper may also be interesting.
"System-size corrections for self-diffusion coefficients calculated from
molecular dynamics simulations: The case of CO2, n-alkanes, and
poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016);
http://dx.doi.org/10.1063/1.4960776
2016-
As I understand it, this error is not dependent on the mdp file, but on
your system. Maybe you need to define a larger system. Of course, you
could try decreasing rlist, but the value of rlist is usually dependent on
the force field you are using, so you risk breaking the physics if you
decrease r
I guess you could try setting all your charges to zero in the topology.
Whether the result tells you something physically meaningful is up to you.
Just my two cents
Victor
2015-10-20 19:46 GMT-05:00 li he :
> in other words, I want to just assume ALL intra-molecular electrostatics
> (charge-cha
healthy discrepancy thresholds.
>
>
>
>
>
> On Thu, Oct 15, 2015 at 6:02 PM, Victor Rosas Garcia <
> rosas.vic...@gmail.com
> > wrote:
>
> > Thanks Justin. That's what I needed to know.
> >
> > Victor
> >
> > 2015-10-15 15:58 GMT-05
Thanks Justin. That's what I needed to know.
Victor
2015-10-15 15:58 GMT-05:00 Justin Lemkul :
>
>
> On 10/15/15 4:51 PM, Victor Rosas Garcia wrote:
>
>> hello everybody,
>>
>> Let us say that I have a topology for a small organic molecule. When
>> r
hello everybody,
Let us say that I have a topology for a small organic molecule. When
running NPT equilibration to determine the density of the solid, I get a
12% error vs experiment. When determining the melting point using simulated
heating, my error is about 15% vs experiment. Are these errors
this list does not accept attachments. Please upload your file to some
file-sharing service and tell us the link.
Victot
2015-10-01 2:21 GMT-05:00 surbhi mahajan :
> Hi,
> I am trying to do simulations using lipids like DPPC and DMPC , i am not
> able to develop a coarse grained model nor am i
Have you tried the option "-pbc whole" instead of "-pbc mol"?
Victor
2015-10-01 6:43 GMT-05:00 gromacs query :
> Hi All,
>
> I have linear polymer in octahedron box and when I try to visualise a
> polymer in octahedraon box then water octahedron box looks as expected but
> my polymer looks broke
You said it yourself: to neutralize the net charge of the system.
Victor
2015-08-20 14:58 GMT-05:00 Jorge Fernandez de Cossio Diaz :
> Since the ion added is usually very far away from the protein (or molecule
> of interest), I don't see how it can affect the results of the molecular
> dynamics
If you mean more than one term for a single dihedral, that would require
function type 9 (see section 4.2.12 in the manual). Otherwise, if you
specify a single dihedral more than once with different function type each
time, I'm not sure what GROMACS would do.
Hope this helps.
Victor
2015-08-17
Hello Soumadwip,
from a quick look, it seems to me that your topology is missing many bonds.
The bonds section specifies atom numbers like "1 403", but I don't see
bonds with atom numbers ranging in the 100's or the 200's. In addition, I
don't see any bond angles defined. I saw distortions simi
it could be, but it might just be easier to try redefining smaller charge
groups and run the dynamics again.
Hope this helps
Victor
2015-08-09 2:16 GMT-05:00 faride badalkhani :
> Dear all,
>
> I am truing to do an MD simulation on dendrimeric structures. I can perform
> all steps successfully,
You can reduce the box size with editconf. If you start with a protein,
you can add a layer of water of a given thickness by using genbox.
Hope this helps
Victor
2015-07-10 0:35 GMT-05:00 James Lord :
> Hi all,
> I have a system with 300k atoms, but computationally it is expensive for me
> doi
IIRC, you do not need to redo the whole run. You can specify the new
energygrps in the mdp file and use "mdrun -rerun" to re-process the results
you already have. Check the manual for the exact syntax.
Hope this helps
Victor
2015-07-02 23:50 GMT-05:00 Dr. Seema Mishra :
> Hello Gromacs users,
Hello,
In your command line you do not specify an index file. Maybe you need to
generate one. Check out usage of make_ndx.
Hope this helps
Victor
2015-06-03 13:41 GMT-05:00 marzieh dehghan :
> Hi every body
>
> I create a covalent bond and now I want to held MD by gromacs,
>
> after holding t
That is not "portability" but "forward compatibility". Not easy to do.
Victor
2015-05-25 7:25 GMT-05:00 Alexey Shvetsov :
> Hi!
>
> Mark Abraham писал 21-05-2015 12:44:
>
>> Hi,
>>
>> There are no known issues with .tpr file portability. By design there
>> should be none.
>>
>
> Except running
if your file is missing only the hydrogens, openbabel can add them for
you. If your file is missing heavier atoms, I don't know.
Hope this helps
Victor
2015-04-13 2:00 GMT-05:00 Ming Tang :
> Dear all,
>
> I got a pdb file including the C-alpha itoms of different residues only. Is
> there any
Perhaps I can be of help here.
Except for the smallest systems, GROMACS simulations are very
compute-intensive, so a single machine is needed for a single job. In
many instances, several machines are required for a single job
(provided you have a fast enough network).
If you give a single machine
OK Justin, thank you for your patience. I'll do as you say.
Have a Happy New Year!
Victor
2015-01-07 10:50 GMT-06:00 Justin Lemkul :
>
>
> On 1/6/15 2:04 PM, Victor Rosas Garcia wrote:
>>
>> Hello everybody,
>>
>> I'm back from the holidays. Still
1mc00/view?usp=sharing
and the resulting (wrong) profile
https://drive.google.com/file/d/0B2K7fedV_ZFzWFB1TURoanB4U2c/view?usp=sharing
Any suggestions?
Victor
2014-12-15 7:24 GMT-06:00 Victor Rosas Garcia :
> OK.
>
> thank you. Time to get to work.
>
> Victor
>
> 2014-12-1
OK.
thank you. Time to get to work.
Victor
2014-12-14 20:42 GMT-06:00 Justin Lemkul :
>
>
> On 12/14/14 9:33 PM, Victor Rosas Garcia wrote:
>>
>> Hello everybody,
>>
>> I'm back. From the last time I tried this, I took all the
>> configurations (all
2014-12-02 20:46 GMT-06:00 Victor Rosas Garcia :
> OK, I'll get to work adding a few more windows.
>
> Thanx Justin
>
> 2014-12-02 17:27 GMT-06:00 Justin Lemkul :
>>
>>
>> On 12/2/14 12:29 PM, Victor Rosas Garcia wrote:
>>>
>>> Hello e
OK, I'll get to work adding a few more windows.
Thanx Justin
2014-12-02 17:27 GMT-06:00 Justin Lemkul :
>
>
> On 12/2/14 12:29 PM, Victor Rosas Garcia wrote:
>>
>> Hello everybody,
>>
>> I'm back.
>>
>> I have redone part of the tutori
The list does not accept attachments. Please upload your files to some
publicly accessible site and provide a link.
Victor
2014-12-02 0:16 GMT-06:00 Seera Suryanarayana :
> Dear Mark
>
> I have used the following command.
> gmx rms -s em.tpr -f em.trr -o rmsd.xvg
>
> I got nothing the graph. You
correct that the final configuration is moved with respect to
the pre-equilibration configuration?
Should I do a longer NPT equilibration of the initial configurations?
Best regards
Victor
2014-11-18 16:31 GMT-06:00 Victor Rosas Garcia :
> Thanks, I'll check it out. It may be a remnant of a previ
My guess is that g_angle is taking the atom order for the bond angle
from the topology.
Hope this helps
Victor
2014-11-28 8:21 GMT-06:00 Cyrus Djahedi :
> Hi all. I'm interested in calculating a specific angle between three atoms
> situated in adjacent cellulose polymer chains. So I made the fo
Thanks, I'll check it out. It may be a remnant of a previous, botched, run.
2014-11-18 15:56 GMT-06:00 Justin Lemkul :
>
>
> On 11/18/14 3:23 PM, Victor Rosas Garcia wrote:
>>
>> Sorry about that Office messup.
>>
>> These are the new links:
>> his
between
different runs, but I do think the difference is large enough to think
something is amiss.
Regards
Victor
2014-11-18 13:14 GMT-06:00 Justin Lemkul :
>
>
> On 11/18/14 10:58 AM, Victor Rosas Garcia wrote:
>>
>> Hello everybody,
>>
>> I have followed Jus
Hello everybody,
I have followed Justin Lemkul's tutorial on umbrella sampling, but
when I do the data analysis, my energy profile looks wrong.
Please see the profile:
https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/profile.png
and the hi
That is the first thing I would do: make the box larger, so the total
pulling distance is less than half the box length.
regards
Victor
2014-11-06 23:40 GMT-06:00 Yixin Ai :
> Dear everyone，
> i want to use gromacs to perform the steered molecular dynamcs
> simulation. My system is the prot
just put the itp file in your working directory, and include it in the
top file of your system, so that Gromacs can find it.
Hope this helps.
Victor
2014-11-02 8:54 GMT-06:00 Kalyanashis Jana :
> Dear all,
> I am trying to run a gromacs simulation using an .itp file of an unknown
> molecule ( no
OK, I'll try that.
thanks for your input
Victor
2014-10-15 16:28 GMT-05:00 Justin Lemkul :
>
>
> On 10/15/14 5:11 PM, Victor Rosas Garcia wrote:
>>
>> but... the lipids I am interested in are not included in the files
>> provided by the authors. I want to mak
but... the lipids I am interested in are not included in the files
provided by the authors. I want to make a new lipid that is compatible
with said forcefield.
Victor
2014-10-15 15:46 GMT-05:00 Justin Lemkul :
>
>
> On 10/15/14 4:40 PM, Victor Rosas Garcia wrote:
>>
>> darn
and.
>
>
> Dr. Vitaly V. Chaban
>
> Виталий Витальевич ЧАБАН
>
>
> On Wed, Oct 15, 2014 at 5:49 PM, Victor Rosas Garcia
> wrote:
>> Hello everybody,
>>
>> I want to build a topology for a lipid to use the parameters reported
>> by Jämbeck and
Hello everybody,
I want to build a topology for a lipid to use the parameters reported
by Jämbeck and Lyubartsev
Jämbeck, Joakim P. M., y Alexander P. Lyubartsev. «Derivation and
Systematic Validation of a Refined All-Atom Force Field for
Phosphatidylcholine Lipids». J. Phys. Chem. B 116, n.o 10
e, since the constant term yields a null derivative)
>
> best
>
> Andre
>
> On Wed, Oct 8, 2014 at 3:50 PM, Victor Rosas Garcia
> wrote:
>
>> Hello everybody,
>>
>> I have calculated ab initio energies for a torsional potential that I
>> want
Hello everybody,
I have calculated ab initio energies for a torsional potential that I
want to fit to a Fourier series. I have calculated the difference
between the ab initio energies and the forcefield with the torsion
potential set to zero (lets call that "diff curve"). This gives me a
somewhat
Hello Stephan,
Do you mean PACKMOL?
http://www.ime.unicamp.br/~martinez/packmol/
VIctor
2014-08-13 0:58 GMT-05:00 lloyd riggs :
> Dear GMX users,
>
> I ran across a nice web page, I believe from a brazilian group, for
> generating membranes of any compnents (pdb). This was months ago, and afte
If you are under Linux, you could use "tail" to get rid of the lines
you don't want. Check "man tail" for details.
Hope this helps
Victor
2014-08-03 17:57 GMT-05:00 Marco Rougeth :
> Hello!
>
> I using grompp and mdrun and the output text shows too much text, like the
> version, contributors na
The error message says that the perl script could not find a file named
confout.gro. Either generate one or put it in the correct directory, so
the script can find it.
Victor
2014-07-04 3:48 GMT-05:00 RINU KHATTRI :
> hello gromacs users now i am at minimization step but one error after the
>
hen run Gromacs, the connection with NFs is lost just few time of
> > > compute. This not happen when run NAMD 2.9 alone.
> > >
> > > And this is the command for the cluster:
> > > nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> > > /op
omacs/bin/mdrun -v -s md.tpr -deffnm md &
>
> I hope can help me!!
> Best regards from Chile.
>
>
> 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia :
>
> > Hello Natalia,
> >
> > The error says that it is trying to change to a directory named
> > /home/
Hello Natalia,
The error says that it is trying to change to a directory named
/home/fmontenegro, but that such a directory does not exist. This is not a
GROMACS error, but a problem related to how the cluster is setup. Your
cluster administrator should be able to help with this problem.
Best re
Hello everybody,
Let's say that I have a torsion potential, calculated at an ab initio level
and I want to develop parameters for GROMACS.
1) As I understand, I have to develop a topology (used acpype for that)
2) Then I took the topology and found all the dihedrals that include my
torsion of inte
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