Hi,
There is not much information to go with, but I can give some general remarks.
Could this not suggest that either your reaction coordinate is not suited,
driving the system into a region of very high potential energy, from where it
can escape though the reaction you consider unreasonable. B
No, but this is possible in Charmm and in Amber.
Best,
Gerrit
> Date: Wed, 18 Dec 2019 11:52:15 +0530
> From: Muneeswaran S
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Constant pH replica exchange MD in Gromacs
> Message-ID:
>
> Content-Type: text/plain; charset="UTF-8"
>
> Good
Dear Vlad,
Tutorials can be found at http://wwwuser.gwdg.de/~ggroenh/software.html
Although the tutorials are outdated and were designed for much older version of
GROMACS, most steps can still be run. Besides, the tutorials should help
getting familiar with the QM/MM input.
A newer tutorial, b
Hi
Good point. The environment variable names changed.
Thus
$GMX_QM_MODIFIED_LINKS_DIR is what used to be DEVIL_DIR
The same for the others.
Gerrit
> Good 4. Re: Gromacs2019 + Gaussian09 QMMM (nikol...@spbau.ru)
>
>
> Dear Gerrit,
>
> Thank you very much for your answer.
> As I under
Dear Dmitrii,
Unfortunately, the group nb-search scheme that was needed for QM/MM is
discontinued. Because it still worked in the 2018 version, I suggest that you
use the previous version until the problem is fixed.
Use
-DGMX_QMMM_PROGRAM=gaussian
in the cmake command to compile with support.
Hi,
I think it will still work if you use the "gau": script found here:
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
best,
Gerrit
On 5/7/19 9:59 PM, ??? wrote:
> Dear Gromacs support,
> I want to install Gromacs 2018.5 with gaussian09 software support in Centos
> system, I try to us
Dear Sergio,
If you're using PME, you need to also include the reciprocal contribution.
Gerrit
Dear gmx comunity,
I am trying to calculate the electrostatic interaction of my system for
force field development. My system consists of 7 positively charged
particles interacting (system A) with
Hi,
For such specific questions, it will be better to directly contact the authors
of that study. Since the paper is not too long ago yet, they might share their
input files with you.
Good luck,
Gerrit
Dear all, I'm doing the QMMM simulation about OH radicals interacting
with DNA's
I live in iran and we don't access to Gaussian.
You think DFTB3 (maybe)could be better choice as it's free?
As I wrote earlier, that depends on whether DFTB3 provides a sufficiently
accurate description for your system. To find that out you need to either
perform a series of benchmarks, or go
Hi,
> Is it free to use Gaussian?( as it's not free software generally)
Gaussian is a commercial program, but perhaps your research group, department,
or computer center etc. have purchased it already.
If you want a free general purpose QM program, you could consider Gamess-US.
When using an
Hi,
You need to compile with the QMMM-flag on
GMX_QMMM_PROGRAM = gaussian
of for older versions --with-qmmm-gaussian
After that you can use the script at to run a QM/MM simulations with any
version of the Gaussian program.
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
Best,
Gerrit
De
Hi,
What is exactly your question?
If it is whether you can use gromacs for QM/MM, the answer is yes.
Whether your QM/MM model it is valid, is always up to you to check, as with any
other pure QM, MM or QM/MM model. Sometimes, the validation for the model can
be found in literature, sometime
Hi,
Unfortunately, for this to work
you need to have both heme and protein in one topology.
best,
gerrit
Tidings and a good day.
Hi,
I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
take it forward. I've found one strategy using a dummy atom in linker.
However, th
Hi,
Did you try if it works?
If not, you can adapt the general gau gaussian script to molpro input
(http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian).
I assume that is also the how the turbomole interface has been done.
Gerrit
Hi,
I am looking for viable systems for doing QM/MM calcula
Hi,
Is the potential energy still going down, despite the rupture of the QM region?
Input is same for EM and MD, and the fact that you can perform QM/MM dynamics
looks promising. Are you using constraints ?
What happens if you do 100 steps of CG, using jus MM,but all other parameters
the same?
Hi,
Could the rupture suggest that perhaps the underlying QM/MM model is somewhat
flawed?
What happens when you run the minimisation without the constraint between the
QM and MM atoms? Do you have convergence problems?
Gerrit
Message: 2
Date: Fri, 2 Mar 2018 13:01:09 +0300
From: nikol...@s
Hi,
It is possible, but only using gromacs' internal optizers: SD(steep), CG, or
BFGS.
And you can only optimise minima, not transition states.
Best,
Gerrit
Message: 3
Date: Thu, 1 Mar 2018 12:44:53 +0300
From: nikol...@spbau.ru
To: gmx-us...@gromacs.org
Subject: [gmx-users] QM/MM optim
It is well documented how to construct topologies for ground states of
molecules and ions. My task is to simulate the behaviour of dye (anion) after
laser exitation in supramolecular complex. Is it possible with standard gromacs
force fields?
Yes this is possible. You just need to fit the par
Hi,
For 1, I can't say, unless I see the input, but it could be that the Link atoms
was not included in the QM groups?
For 2, make sure the virtual_sites2 entry is complete, i.e.: Linkatom QMatom MM
atoms 1 d(QMatom-Linkatom)/d(QMatom-MMatom)
The latter is thus the fraction between the two b
r help.
Best regards,
Zoe
On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit
mailto:ggro...@gwdg.de>> wrote:
>From the error message it seems that ORCA program crashes. Unfortunately, Orca
>is no longer supported, which means that if the ORCA's input or anything else
>has change
>From the error message it seems that ORCA program crashes. Unfortunately, Orca
>is no longer supported, which means that if the ORCA's input or anything else
>has changed, the gromacs interface may fail.
What you could try is to use the version of ORCA that others have used before.
Best,
Gerr
Hi,
The negative Coulomb energy is due to the interaction of your positively
charged Argon atoms with the background charge of +10. However, I nevertheless
expect that the dynamics will be that of all atoms repelling, as the uniform
background charge does not exert a force in your case. Also, y
Hi,
the problem is that I am not able to compile MOPAC7 correctly. Some routines
work, but not all and lead to erroneous results.
If you need to run MD with semi empirical methods, I recommend using gaussian
instead.
best,
Gerrit
Message: 3
Date: Thu, 12 Oct 2017 10:24:33 +0900
From: minky
Hi,
Could it be that the QM level of theory is not suited (candidates are charge
and multiplicity) for the QM subsystem? What happens if you run a QM only
calculation on your QM system ?
Gerrit
Dear gmx users
I'm doing an QM/MM simulation of a ligand-protein system by the Gromacs
ORCA interfa
Hi,
On 22/02/17 13:15, Sameer Edirisinghe wrote:
> Dear Users,
>
> I need to simulate my polymer system under UV radiation ( or photons) as i
> want to study the UV behavior of the polymer system. Can anyone please
> suggest me a method to do that with gromacs.
>
>
> Regards
> Bhagya Karunarathna
ithout
problems.
Greetings
Sylwia
On 07.11.2016 14:50, Groenhof, Gerrit wrote:
> Hi,
>
> Do I understand correctly that the grompp complains about a bond that is
> still bond type 1?
>
> If so, then the error message suggests that grompp cannot access a ff*bin.itp
> with the param
runs without
problems.
Greetings
Sylwia
On 07.11.2016 14:50, Groenhof, Gerrit wrote:
> Hi,
>
> Do I understand correctly that the grompp complains about a bond that is
> still bond type 1?
>
> If so, then the error message suggests that grompp cannot access a ff*bin.itp
> w
j fuc0, c1, ...
...
21 22 5 ; C9A N10
22 23 5 ; N10 C1' ;'
24 23 1 ; C2' C1'
24 25 1 ; C2' O2'
There is no error for atoms with bond type 5, but for all with bond type 1.
Greetings
Sylwia
On 11/05/2016 03:40
Is the LA also defined for the force field you're using? Can you check whether
there is a LA entry in the ff*nb.it of the force field? If not, add it there
manually.
Best,
gerrit
Message: 2
Date: Fri, 4 Nov 2016 16:10:03 +0100
From: Sylwia Kacprzak
To: gromacs.org_gmx-users@maillist.sys.kth.s
ination in ORCA_GTOInt
Segmentation fault (core dumped)
I dont know what is wrong, because i am running the calculation on just one PC
many thanks
Aliyu Adamu
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillis
Changing the cut-off scheme to group should fix the first issue. In fact, that
is also what the output seems to suggest...
The second issue suggests that you grompp does not have access to the correct
force field files. Proving information on where the *.itp files are should
solve that issue to
depending on the shell try using "export BASENAME=topol" or "setenv BASENAME
topop' instead. You can check if things worked by typing echo $BASENAME which
should be topol.
I am surprised you did not get an error message form the shell after typing
these lines...
Gerrit
Message: 3
Date: Tue, 1
At the moment only gaussian is supported and maintained in the release versions
of gromacs. The most convenient way is to compile gromacs for QM/MM support
with gaussian, and use the "gau" script at
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian.
Best,
Gerrit
Hello All,
Please can anyone
; So the only QM software that GROMACS can run for QMMM is Gaussian (09?),
> in single-thread CPU-only mode and with cut-off setting that's listed as
> depreciated, right?
> 08.09.2016 21:11, gromacs.org_gmx-users-requ...@maillist.sys.kth.se ?:
> > Message: 3
> > Date: T
So the only QM software that GROMACS can run for QMMM is Gaussian (09?),
in single-thread CPU-only mode and with cut-off setting that's listed as
depreciated, right?
Yes, that's correct.
Note that although mdrun will use a single thread, gaussian, you use as many
CPUs as it can handle.
Furt
Hi,
Orca with gromacs >= 5 has not been tested and there are some indications that
it is broken (redmine issue 1934).
QM/MM with Gaussian is working, as long as you use a group based cut-offs and
run mdrun on a single thread (-nt 1).
I therefore recommend to use gaussian (with the gau script a
1 Aug 2016 13:28:56 -0600
From: Clinton King
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
Gerrit)
Message-ID:
Content-Type: text/plain; charset=UTF-8
Is is true that the gau script available at http://wwwuser.gw
Hi,
Unless there are no atoms in the QM region, the QM energy should not be zero.
Can you confirm that mdrun writes an input file (input.com)? and gaussian is
executed?
If not, has gromacs been compiled with QMMM support
(GMX_QMMM_PROGRAM:STRING=gaussian)?
Best,
Gerrit
Hi,
Sadly, most of
INdeed, ORCA is not maintained at the moment. At least not by me, partially
because it is not opensource (AFAIK).
The interface with gaussian is still working though. So my (poor) advice is
either to keep using an older version of gromacs, or switch to gaussian,
depending on the functionality y
Otherwise you may try your luck with the ATB server for Gromos topologies:
https://atb.uq.edu.au
Gerrit
Hi,
There's a collection of contributed stuff on the GROMACS webpage, so good
luck with that... But mostly it's a matter of people choosing to share.
Authors of papers where such have been u
To enable QM/MM with Gaussian compile gromacs with
GMX_QMMM_PROGRAM:STRING=gaussian
If you have compiled already you can change that in you CMakeCache.text for
example and recompile.
After that you can use the gau script. You need to set $GMX_QM_GAUSS_DIR to the
location of that script and
GM
You always need to neutralise with counter-ion, rather than rely on the uniform
background charge that the PME method introduces if your system is charged. The
background charge introduces artefacts for non-homogeneous systems by placing
charge uniformly across the system rather than inside the
aring
https://drive.google.com/file/d/0B-W4G39j_IcjZlVPb1NySkUtRDQ/view?usp=sharing
(Please let me know if the links above don't work.)
Thanks for your help
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
> Message: 2
> Date: Sun, 12 Jun 2016 05:16:13 +
>
Hi,
Which version of Gmx are you using?
I ask because of a recent bug fix. The bug was that I tried to print the value
of an environment variable, without checking if that variable was set, causing
set faulting.
Make sure the GMX_QM_GAUSS_DIR (for Gmx < 5 GAUSS_DIR) are set and point to the
l
Hi,
this is weird. I assume you've put the *'s only in your email?
Could you send me (off list) the mdp, index, top and gro file? Perhaps
something else, such as missing link atom triggers the error message
incorrectly.
Gerrit
Subject: [gmx-users] QMMM grompp error atom numbers fields.
Messa
You need to make one topology for your protein that includes all atoms that you
want to treat with QM. If your QM region includes part of the protein and the
ligand, you can most easily make one topology with the -merge option of pdb2gmx.
Gerrit
Dear Gromacs Users,
I am interested to know how
All interactions between QM atoms are excluded automatically, except the [
bonds ], in case you want to keep these constrained. If do not want to
constrain the bonds, you have to manually put the bond type to 5
Gerrit
3. qmmm question (andrian)
Message: 3
Date: Tue, 10 May 2016 16:12:45
hed all my
simulation files... hope someone can help.. thanks in advance
cheers
On 27/04/16 01:48, Groenhof, Gerrit wrote:
> Hi,
>
> Are you able to run a stable MM simulation with that system?
>
> Can you rule out that the system is not strained somewhere?
>
> Where do the
Hi,
Are you able to run a stable MM simulation with that system?
Can you rule out that the system is not strained somewhere?
Where do the starting coordinates come from?
best,
Gerrit
Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian
To: gromacs.org_gmx-users@maillist.sys.kth.s
Hi again,
>From the error message it seems that the virtual_sites are not in the same
>topology file. Since introduction of molecular topologies in GMX4, all QM
>atoms must be in the same topology entry. It appears that in your case there
>is a stretch of atoms, perhaps waters, in between the l
Hi,
Indeed, Link atoms have to be added to the .gro file. The atom indexing in the
.gro file is not used, so no need to renumber. A simple editconf can do that
for you if too, if you would like to have the numbering correct. However, you
need to adjust the total number of atoms at the top of t
Hi,
The problem is that the QM/MM code checks all bonded interactions until 4
atoms, which at the time it was implemented, was the maximum, i.e. before CMAP.
However, I am not sure whether the CMAP interactions should be in or excluded.
Excluding will alter the backbone energetics in your QM/C
Perhaps it was unintentional, but if you really understood the rules, you'd
also understand there is no need to insult. In particular not those who are
trying to help.
Plus, you'd better take all of your time to read and understand the paper
you're linking to as it precisely prescribes how to c
al on DNA:
http://wwwuser.gwdg.de/%7Eggroenh/SaoCarlos2008/html/tutorial.html
> Message: 1
> Date: Tue, 10 Nov 2015 11:31:03 +
> From: "Groenhof, Gerrit"
> To:"gromacs.org_gmx-users@maillist.sys.kth.se"
>
I'm looking to try a QM/MM simulation for a protein-DNA system using
Gussian09 & GROMACS 4.6 (these are available at the local cluster).
Does anyone has any experience working and getting results in this
environment? Are there any notable problems? Should I pay special
attention to any particular
Hi,
> Albert,
>
> Gromacs won't automatically neutralize the system (as far as I know). If I
> recall being non-neutral doesn't necessarily result in problems, but may
> instead slow your run-time. I am sure someone will correct me if I am wrong.
>
> Old posts suggest that GROMACS does in fact
Hi,
Instead of the flag to Cmake you could also manually modify CMakeCache.txt
//QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess,
// orca
GMX_QMMM_PROGRAM:STRING=dftb
best,
Gerrit
Message: 4
Date: Thu, 8 Oct 2015 09:51:38 +0530
From: Padmani Sandhu
To: "gmx-us...@gromacs.org
Hi,
> Hello justin,
>
> Thanks, actually I want to study movement of protons along the lenght of a
> water channel.
>
> What you need is constant-pH MD, which is not natively supported in GROMACS.
What Justin says. There is only a 3.3 version that currently supports this,
which is available at:
Hi,
Since bonds break and form upon proton transfer it requires quantum mechanics,
both for the electrons and the proton(s).
To avoid the heavy computational burden, one can opt to use classical dynamics
for the proton and semi-empirical methods, which are accessible in Gromacs (<5)
through t
5. Re: how to calculate ESP at certain position (Zhenyu Meng)
Haven't given it much thought, but if it is only one or few locations you're
interested in, can't you simply place a +1 e charged dummy atom at that
location in your system and re-compute the total electrostatic energy?
To cor
Yes, you need gaussian09, which has SCC-DFTB implemented and use the QM/MM
interface script available from
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
Some changes will be needed to let the script select DFTB as the method, which
are explained in the script. The modifications require dec
1. Linking Gamess-US with gromacs (Akshay Bhatnagar)
2. Re: Linking Gamess-US with gromacs (Alex)
3. Re: Linking Gamess-US with gromacs (Alex)
4. Re: Linking Gamess-US with gromacs (Alex)
5. Re: Linking Gamess-US with gromacs (Alex)
6. interval simulation (Golnaz Roudsari)
---
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