Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling?

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.

Re: [gmx-users] Constant pH replica exchange MD in Gromacs (Muneeswaran S)

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

Re: [gmx-users] QM/MM run tips or tutorials (Bogdanov, Vladimir)

Dear Vlad, Tutorials can be found at http://wwwuser.gwdg.de/~ggroenh/software.html Although the tutorials are outdated and were designed for much older version of GROMACS, most steps can still be run.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,

Re: [gmx-users] Gromacs2019 + Gaussian09 QMMM (nikol...@spbau.ru)

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

Re: [gmx-users] Gromacs2019 + Gaussian09 QMMM

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

Re: [gmx-users] Gromacs2018.5 install with gaussian09 for QM/MM

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

Re: [gmx-users] PME constant shifts. (Sergio Perez)

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)

Re: [gmx-users] GROMACS/CPMD QMMM do not occur the process of the hydrogen abstraction reaction (limingru)

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

Re: [gmx-users] Qmmm (rose rahmani) (Rose)

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

Re: [gmx-users] Qmmm (rose rahmani)

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

Re: [gmx-users] Gromacs installation to do coupled QMMM with Gaussian (Maryam Kowsar)

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

Re: [gmx-users] Qmmm (rose rahmani)

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,

Re: [gmx-users] QM-MM (sai manohar)

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,

Re: [gmx-users] 3. gromacs with turbomole? (Francesca L?nstad Bleken)

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

Re: [gmx-users] QM/MM optimization in gromacs/gaussian (nikol...@spbau.ru)

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

Re: [gmx-users] QM/MM optimization in gromacs/gaussian

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:

Re: [gmx-users] QM/MM optimization in gromacs/gaussian (nikol...@spbau.ru)

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

Re: [gmx-users] topology for exited electronic state (dgfd dgdfg)

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

Re: [gmx-users] Link atoms issue: QMMM simulation (Zachary Smithline)

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

Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

the crash? Again, thank you for your help. Best regards, Zoe On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit <ggro...@gwdg.de<mailto:ggro...@gwdg.de>> wrote: >From the error message it seems that ORCA program crashes. Unfortunately, Orca >is no longer supported, which means t

Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

>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,

Re: [gmx-users] non-neutral system

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,

Re: [gmx-users] problem about installing the latest version of MOPAC (minky son)

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:

Re: [gmx-users] QM/MM simulation (Mostafa Javaheri)

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

Re: [gmx-users] UV radiation (David van der Spoel)

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

Re: [gmx-users] qm/mm LA not found

. 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 parameters for the a

Re: [gmx-users] qm/mm LA not found

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 >

Re: [gmx-users] qm/mm LA not found (Sylwia Kacprzak)

, ... ... 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 PM, Groenhof, Gerrit wrote: > Is the LA a

Re: [gmx-users] qm/mm LA not found

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

Re: [gmx-users] qmmm

___ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Groenhof, Gerrit [ggro...@gwdg.de] Sent: Tuesday, November 1, 2016 12:45 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-user

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 150, Issue 127

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

Re: [gmx-users] qmmm

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,

Re: [gmx-users] QM/MM (Adamu, Aliyu)

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

Re: [gmx-users] About the QM/MM MD of Gromacs

16 21:11, gromacs.org_gmx-users-requ...@maillist.sys.kth.se ?: > > Message: 3 > > Date: Thu, 8 Sep 2016 13:05:38 + > > From: "Groenhof, Gerrit"<ggro...@gwdg.de> > > To:"gromacs.org_gmx-users@maillist.sys.kth.se" > > <gromacs.or

Re: [gmx-users] About the QM/MM MD of Gromacs (???) (Timofey Tyugashev)

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.

Re: [gmx-users] About the QM/MM MD of Gromacs (???)

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

Re: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) (Clinton King)

2016 13:28:56 -0600 From: Clinton King <clintonkin...@chem.byu.edu> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) Message-ID:

Re: [gmx-users] QM/MM simulations (Mark Abraham)

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

Re: [gmx-users] Gromacs Orca QMMM segfault

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

Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids

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

Re: [gmx-users] Gaussian/GROMACS (? ?)

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

Re: [gmx-users] interfacing with Gaussian 09

rive.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 + > From: "Groenhof, Gerrit&qu

Re: [gmx-users] interfacing with Gaussian 09 (Mark Abraham)

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

Re: [gmx-users] QMMM grompp error atom numbers fields.

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.

Re: [gmx-users] Making separate topology file for QM atoms (bharat gupta)

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

Re: [gmx-users] gmx-users qmmm question (andrian)

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

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian) (andrian)

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 starting

Re: [gmx-users] Defining LA atoms in .gro file

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

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119

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

Re: [gmx-users] Fw: question:Justin toturial (Mass)

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

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 45

http://wwwuser.gwdg.de/%7Eggroenh/SaoCarlos2008/html/tutorial.html > Message: 1 > Date: Tue, 10 Nov 2015 11:31:03 + > From: "Groenhof, Gerrit"<ggro...@gwdg.de> > To:"gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillis

Re: [gmx-users] 2. QM/MM (Timofey Tyugashev)

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

Re: [gmx-users] PME on a non-neutral system

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

Re: [gmx-users] addition of hydronium ion in simulation box

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

Re: [gmx-users] 2. Proton transfer reaction in gromacs (Padmani Sandhu)

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

Re: [gmx-users] Fwd: DFTB implementation (Vitaly V. Chaban)

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