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

2020-02-20 Thread Groenhof, Gerrit
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

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

2019-12-17 Thread Groenhof, Gerrit
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)

2019-10-24 Thread Groenhof, Gerrit
Dear Vlad, Tutorials can be found at http://wwwuser.gwdg.de/~ggroenh/software.html Although the tutorials are outdated and were designed for much older version of GROMACS, most steps can still be run.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

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

2019-10-07 Thread Groenhof, Gerrit
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

Re: [gmx-users] Gromacs2019 + Gaussian09 QMMM

2019-09-30 Thread Groenhof, Gerrit
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.

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

2019-05-09 Thread Groenhof, Gerrit
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

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

2019-03-29 Thread Groenhof, Gerrit
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

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

2018-09-25 Thread Groenhof, Gerrit
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)

2018-08-06 Thread Groenhof, Gerrit
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)

2018-08-06 Thread Groenhof, Gerrit
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

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

2018-08-06 Thread Groenhof, Gerrit
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

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

2018-08-05 Thread Groenhof, Gerrit
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

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

2018-05-28 Thread Groenhof, Gerrit
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

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

2018-05-03 Thread Groenhof, Gerrit
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

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

2018-03-16 Thread Groenhof, Gerrit
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?

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

2018-03-02 Thread Groenhof, Gerrit
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

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

2018-03-01 Thread Groenhof, Gerrit
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

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

2018-01-02 Thread Groenhof, Gerrit
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

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

2017-12-02 Thread Groenhof, Gerrit
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

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

2017-11-29 Thread Groenhof, Gerrit
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

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

2017-11-27 Thread Groenhof, Gerrit
>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

Re: [gmx-users] non-neutral system

2017-11-06 Thread Groenhof, Gerrit
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

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

2017-10-12 Thread Groenhof, Gerrit
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

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

2017-08-28 Thread Groenhof, Gerrit
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

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

2017-02-22 Thread Groenhof, Gerrit
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

2016-11-08 Thread Groenhof, Gerrit
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

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

2016-11-07 Thread Groenhof, Gerrit
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

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

2016-11-07 Thread Groenhof, Gerrit
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

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

2016-11-05 Thread Groenhof, Gerrit
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

Re: [gmx-users] qmmm

2016-11-02 Thread Groenhof, Gerrit
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

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

2016-11-01 Thread Groenhof, Gerrit
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

Re: [gmx-users] qmmm

2016-11-01 Thread Groenhof, Gerrit
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

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

2016-10-20 Thread Groenhof, Gerrit
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

2016-09-10 Thread Groenhof, Gerrit
; 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

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

2016-09-09 Thread Groenhof, Gerrit
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

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

2016-09-08 Thread Groenhof, Gerrit
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

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

2016-09-01 Thread Groenhof, Gerrit
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

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

2016-08-29 Thread Groenhof, Gerrit
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

Re: [gmx-users] Gromacs Orca QMMM segfault

2016-06-24 Thread Groenhof, Gerrit
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

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

2016-06-23 Thread Groenhof, Gerrit
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

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

2016-06-20 Thread Groenhof, Gerrit
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

Re: [gmx-users] to neutralize the system

2016-06-14 Thread Groenhof, Gerrit
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

Re: [gmx-users] interfacing with Gaussian 09

2016-06-13 Thread Groenhof, Gerrit
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 + >

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

2016-06-11 Thread Groenhof, Gerrit
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

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

2016-05-24 Thread Groenhof, Gerrit
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

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

2016-05-13 Thread Groenhof, Gerrit
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)

2016-05-10 Thread Groenhof, Gerrit
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

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

2016-04-28 Thread Groenhof, Gerrit
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

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

2016-04-26 Thread Groenhof, Gerrit
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

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

2016-04-22 Thread Groenhof, Gerrit
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

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

2016-04-21 Thread Groenhof, Gerrit
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

Re: [gmx-users] QM/MM error: no such bonded interactions with 5 atoms (Mark Abraham)

2016-03-10 Thread Groenhof, Gerrit
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

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

2016-02-01 Thread Groenhof, Gerrit
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

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

2015-11-11 Thread Groenhof, Gerrit
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" >

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

2015-11-10 Thread Groenhof, Gerrit
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

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

2015-10-21 Thread Groenhof, Gerrit
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] Dftb as qmmm method with gromacs

2015-10-08 Thread Groenhof, Gerrit
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

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

2015-09-21 Thread Groenhof, Gerrit
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:

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

2015-08-11 Thread Groenhof, Gerrit
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

Re: [gmx-users] how to calculate ESP at certain position (Zhenyu Meng)

2015-08-04 Thread Groenhof, Gerrit
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

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

2015-08-03 Thread Groenhof, Gerrit
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

Re: [gmx-users] Linking Gamess-US with gromacs (Akshay Bhatnagar)

2015-06-29 Thread Groenhof, Gerrit
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) ---