Re: [gmx-users] qmmm and "real-life" meaning of null

2012-06-08 Thread Gerrit Groenhof
Hi, INdeed, you would still need a LJ term for the QM atoms, in order to interact with the MM atoms. Only if the radius around your special atom were larger than the LJ cut-off could you safely ignore the LJ paramter. gerrit > > Message: 3 > Date: Thu, 07 Jun 2012 19:47:02 -0400 > From: "Just

[gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas)

2012-06-08 Thread Gerrit Groenhof
YOucan only use one thread in mdrun, but more than one in ORCA. Try to estimate the ratio of computation time spent between the QM and MM calculation to get an idea of why we never bothered to parallellize the MM part. Hope this helps, Gerrit > > 4. QM/MM Calculation with Orca (Minos Matso

[gmx-users] Re: on MD at constant pH (Acoot Brett)

2012-03-28 Thread Gerrit Groenhof
You could have a look at Donnini et al, JCTC 7 (2011), 1962-1978 And with teh code available from http://www.mpibpc.mpg.de/home/grubmueller/projects/Methods/ConstpH/index.html give it a try for your problem. Gerrit > > 1. on MD at constant pH (Acoot Brett) > > > Dear All, > > Currently

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 56

2011-12-10 Thread Gerrit Groenhof
Does this also happen if you use pbc? gerrit On 10 Dec 2011, at 10:59, gmx-users-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gm

[gmx-users] Re: itp file for D2O (cuong nguyen)

2011-12-07 Thread Gerrit Groenhof
Please check the paper by Grigera JCP 2001 114 8064 for the derivation for this model. [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OD 1SOL OW 1 -0.8715.99940 2

[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

2011-11-21 Thread Gerrit Groenhof
On 11/22/2011 04:02 AM, gmx-users-requ...@gromacs.org wrote: gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit 2. Re: GROMACS/ORCA QMMM (Jose Tusell) Does anyone know what is going on with the coordinates of the QM region? Why are they not converted to

[gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

2011-11-17 Thread Gerrit Groenhof
> > 3. Re: gromacs/mopac compilation: linking libmopac (Javier Cerezo) Dear Javier, Thanks for this update and your efforts. Can i put it on the website? Could you check however the outcome (energy and forces) of an am1 or pm3 computations with another program? Best wishes, Gerrit > > Hi

[gmx-users] Re: orca and Segmentation fault (xi zhao)

2011-11-14 Thread Gerrit Groenhof
THe error message is clear: your spin multiplicity is 0, which is impossible. Please make sure you understand the basics of electronic structure theory. To test this, you can run the QM system only in stand along QM package. gerrit 2. Re: orca and Segmentation fault (xi zhao) 3. RE

[gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao)

2011-11-08 Thread Gerrit Groenhof
Did you run also your QM subsystem with the stand-alone version of Orca? 6. ORCA and dummy atom in the gromacs (xi zhao) Gerrit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppo

[gmx-users] Re 1. orca and qm/mm (xi zhao)

2011-11-07 Thread Gerrit Groenhof
Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to >

Re: [gmx-users] constant PH simulations

2011-09-07 Thread Gerrit Groenhof
> > Message: 1 > Date: Wed, 07 Sep 2011 12:01:00 +0200 > From: "Emanuel Peter" > Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations > To: > Message-ID: <4e675cfc02f100014...@gwsmtp1.uni-regensburg.de> > Content-Type: text/plain; charset="iso-8859-1" > > At first I would li

Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)

2011-09-06 Thread Gerrit Groenhof
> > 2. Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter) > > Message: 2 > Date: Tue, 06 Sep 2011 15:49:28 +0200 > From: "Emanuel Peter" > Subject: Antw: Re: Re: [gmx-users] constant PH simulations > To: > Message-ID: <4e66410802f100014...@gwsmtp1.uni-regensburg.de> > Con

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 114

2011-05-17 Thread Gerrit Groenhof
> > 3. QMMM+NMA (Yao Yao) > > Hi Gmxers, > > I am wondering if NMA has been introduced into QMMM part of gromacs. > I am trying to get vibrational frequencies of proteins by normal mode > analysis (NMA) in the framework of QMMM. This is not possible, unless your system is so small that you

[gmx-users] Re:qmmm temp definition + linking atom

2011-05-10 Thread Gerrit Groenhof
The link atom can be placed anywhere at step 0. These atom are treated like virtual sites and will thus be placed at the defined position along the QM/MM bond that needs capping. Concerning the temperature, one can treat the QM atoms as a separate group indeed. But as Mark said, why not expo

[gmx-users] Re: gmx-users Digest, Vol 84, Issue 177

2011-04-21 Thread Gerrit Groenhof
> > 4. PYP Connection (Taylor Kaplan) Are the connections between the chromophore and cysteine there? You can check this by scanning your topology file for the indices of the sulphur and C1 atom in the [ bonds ] section. You can use the specbond the attach the chromophore to the protein. T

[gmx-users] Re: Parameterization of a molecule containing a radical, (oxygen) (Justin A. Lemkul)

2011-03-23 Thread Gerrit Groenhof
There is a AMBER FF for this kind of nitroxide spin labels. See PCCP 12 (2010) 11697. Hope it helps, Gerrit Simone Cirri wrote: Hi all, I have a question regarding a new parameterization: actually, I'm wondering whether or not it is possible to do it. The molecule is tempol; you cand find

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 63

2011-03-09 Thread Gerrit Groenhof
The choice for the QM package depends on what level of QM theory you wish to use and what package are available to you. to proceed sue the instructions http://wwwuser.gwdg.de/~ggroenh/qmmm.html Be aware though that QMMM is not to be considered a black box method. Gerrit 4. QMMM (Haresh

[gmx-users] Re: 4. Re: QMMM (Txema Mercero)

2011-03-09 Thread Gerrit Groenhof
Please be more specific than not successful. And also please understand that there are two things involved: the installation, which is so complicated because the gaussian license forbids distrubution of source code. The actual QM, which sometimes is not thought through well enough. A genera

[gmx-users] Re: gmx-users Digest, Vol 82, Issue 189

2011-02-24 Thread Gerrit Groenhof
Since this is a gaussian related question why do you ask it at the gromacs user list? Anyway, the problem you have is that you have inserted a space between the 6-31 and G in the basisset specification. Gaussian has been kind enough to tell you this (see the ' in the second line of the error).

Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

2011-02-17 Thread Gerrit Groenhof
gromacs.org/Documentation/Errors --- "I Used To Care, But Things Have Changed" (Bob Dylan) On 02/17/2011 10:39 AM, Txema Mercero wrote: Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhof wrote: 2. Re: Re: grom

[gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

2011-02-17 Thread Gerrit Groenhof
> 2. Re: Re: gromacs QM/MM compilation with gaussian (Txema > Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppor

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

2011-02-16 Thread Gerrit Groenhof
3/lib/intel64/libintlc.so.5 > 2b0e5d476000-2b0e5d479000 rw-p 0003a000 00:17 6783121 > /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5 > 2b0e5d479000-2b0e5d8b9000 rw-p 2b0e5d479000 00:00 0 > 2b0e6000-2b0e60021000 rw-p 2b0e6000 00:00 0 > 2b0e60021000-2b0e6400 ---p 2b

[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

2011-02-16 Thread Gerrit Groenhof
Are you trying to run with more than one thread? If so, try mdrun -nt 1 Gerrit > > 1. Re: gromacs QM/MM compilation with gaussian (Txema Mercero) > 2. Re: Periodic Boundary Conditions g_mindist -pi (ifat shub) > 3. Re: Re: Periodic Boundary Conditions g_mindist -pi (Mark Abraham) > > >

[gmx-users] Re: QMMM with ORCA

2011-01-27 Thread Gerrit Groenhof
Dear Xiaohu, Thanks for bringing this up. The comment has been there for ever. Since I could not think of an application where one would not be using pbc at the time. However, your clusters prove me wrong. In any case, as a work-around, you may want to use a bigger box, with long enough cut-of

[gmx-users] 4. Requesting advice on pressure scaling in a protein-in-membrane system. (Daniel Adriano Silva M)

2011-01-07 Thread Gerrit Groenhof
Can you simulate the membrane and protein seperately, thus the two system you are trying to merge? Gerrit > > 4. Requesting advice on pressure scaling in a > protein-in-membrane system. (Daniel Adriano Silva M) > > > Dear gmx users and developers, > > I am facing a problem that is new

[gmx-users] Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko)

2010-12-08 Thread Gerrit Groenhof
Try to run with mdrun -nt 1 1. Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko) 2. group temperatures and kinetic energies (Dmitri Dubov) 3. Re: group temperatures and kinetic energies (Dmitri Dubov) -

[gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)

2010-12-07 Thread Gerrit Groenhof
Dera gromacs users, I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. When I run DFT I got an error: number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault Are you tryin

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 41

2010-12-06 Thread Gerrit Groenhof
PAC > LIBS=-lmopac LDFLAGS=-L/usr/local/lib > if i use --with-qmmm-mopac i end in make error (compilation error) > also how to check how to check the link of mdrun aganist libmopac.a is > there is any command for this? > i am expecting your precious reply thanks in advance &g

Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)

2010-12-05 Thread Gerrit Groenhof
Please check if your stand-alone mopac binary works properly. Also check if the mdrun binary is linked against the libmopac.a Gerrit Message: 2 Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST) From: vidhya sankar Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar) To: gmx-users@gromacs

[gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)

2010-12-05 Thread Gerrit Groenhof
i5 > what could i do to remove this error > ? > i am expecting your reply soon thanks in advance > > > -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Subject: Re: [gmx-users] GFP chromophore topology help

2010-11-13 Thread Gerrit Groenhof
gt; >>> >>> >>> >> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech &g

[gmx-users] Re: gmx-users Digest, Vol 78, Issue 123

2010-10-18 Thread Gerrit Groenhof
3. Simulation parameter problem about protein unfolding (Chen) Hi, You write it yourself: In paper you mention, they have used a 0.8 nm cutoff range for both electrostatics and cutoff. You are doing something different by using PME for the electrostatics. Also you are using a much lon

[gmx-users] Re: gmx-users Digest, Vol 77, Issue 142

2010-09-22 Thread Gerrit Groenhof
Why do you try to do MP2. Mopac will only allow semi-empirical methods. Though that does not seem to be the source of the error. Gerrit further when i run Mdrun after energy minimisatins by following command ./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log I got errror as fo

[gmx-users] QM/MM topology fiels problem

2010-09-21 Thread Gerrit Groenhof
Please read the error message: it says that you need no parameters for your conn bonds. Gerrit Message: 2 Date: Tue, 21 Sep 2010 14:58:40 +0530 (IST) From: vidhya sankar Subject: [gmx-users] QM/MM topology fiels problem To: gmx-users@gromacs.org Message-ID:<277598.19746...@web95503.mail.in

[gmx-users] Re: eg compilation problem in Mopac gromacs (vidhya sankar)

2010-09-08 Thread Gerrit Groenhof
rface = 0 >> optimize_fft = no >> ; Temperature coupling >> tcoupl = nose-hoover >> tc-grps = Protein Non-Protein >> tau_t= 0.2 0.2 >> ref_t= 300 300 >&g

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 183

2010-06-30 Thread Gerrit Groenhof
mult=3 > Dihedral around 1109, not found in topology. Using mult=3 > Dihedral around 1115,1122 not found in topology. Using mult=3 > Dihedral around 1126,1133 not found in topology. Using mult=3 > > is this rama.xvg file true and intact? > -- next part ---

Re: Subject: [gmx-users] error compiling mopac and gromacs

2010-06-12 Thread Gerrit Groenhof
> URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100612/ed0e12b1/attachment.html > > -- > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the

[gmx-users] Re: Compile gromacs 4.0.7 with mopac (Stefan Hoorman)

2010-05-27 Thread Gerrit Groenhof
> > > 1. Re: Non-conservation of total energy while using structure > file to resume the simulation (Mark Abraham) > 2. Compile gromacs 4.0.7 with mopac (Stefan Hoorman) Try linking with g2c. Best wishes, Gerrit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

[gmx-users] Re: 2. protein in dppc (edmund lee)

2010-02-23 Thread Gerrit Groenhof
Hi, If I am allowed to do some advertisement: you could try the tool g_membed for inserting proteins as well http://wwwuser.gwdg.de/~ggroenh/membed.html Gerrit gmx-users-requ...@gromacs.org wrote: >2. protein in dppc (edmund lee) > > Date: Tue, 23 Feb 2010 15:55:36 +0800 > From: edmund le

[gmx-users] Re: 1. Need small well known QM/MM example (Ake Sandgren)

2010-02-11 Thread Gerrit Groenhof
Hi Ake, you can download two files at wwwuser.gwdg.de/~ggroenh/ffamber03.tar.gz and wwwuser.gwdg.de/~ggroenh/qmmm_input.tar.gz First is the forcefield files (GMXLIB shoul point there) second is qmmm input files for a QM/MM simulation. Hope it helps. Gerrit > > Message: 1 > Date: Thu, 11 Fe

[gmx-users] Weird error message from QM/MM run. (yoochan,myung)

2010-01-25 Thread Gerrit Groenhof
Could you provide more information? >3. Weird error message from QM/MM run. (yoochan,myung) >4. Re: Re: Re: Fw: Re: Polymer-protein problem (Mark Abraham) >5. Re: gas adsorption on CNT (Mark Abraham) >6. simulation crash with GROMOS96 force field (Vitaly V. Chaban) > -- gmx-use

Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works.

2010-01-22 Thread Gerrit Groenhof
1.166 -1.607 -3.796 > ATOM 13 HE1 TRP1 1.401 -2.473 -4.259 > ATOM 14 CE2 TRP11.673 -0.432 -4.078 > ATOM 15 CE3 TRP11.485 1.803 -3.344 > ATOM 16 HE3 TRP11.065 2.575 -2.699 > ATOM 17 CZ2 TR

[gmx-users] Re: Configuration of Gaussian for QM/MM

2010-01-15 Thread Gerrit Groenhof
The instruction says: To find the fortran source file that contains the function you need, you can use the grep command: grep -i d1e $GAUSS_DIR/*.F What is it that you do misunderstand about this? Gerrit Is there any misunderstand about instruction ? -- gmx-users mailing listgmx-users@gr

[gmx-users] 4. Re: access code for qmmm (Mark Abraham)

2009-11-21 Thread Gerrit Groenhof
You need a newer version to run ORCA: 1016:42git clone git://git.gromacs.org/gromacs 1116:44cd gromacs/ 1216:44git branch --track qmmm origin/qmmm 1316:44git checkout qmmm 1416:44git pull Gerrit On 21 Nov 2009, at 14:16, gmx-users-requ...

[gmx-users] Re: access code for qmmm (Farzad Molani)

2009-11-17 Thread Gerrit Groenhof
for academic user. Thanks in advance Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009821 2306 4280 Fax: 009821 2285 3650 Web: http://www.kntu.ac.ir -- -- Gerrit Groenh

[gmx-users] Re: 1. Normal mode analysis of pure water (simon sangma)

2009-10-20 Thread Gerrit Groenhof
If you are interested in the IR spectrum of water, all you need to do is a simulation of a flexible water model (not flexspc btw), save every fs, compute the dipole moment, compute the powerspectrum of that dipole moment and check for the peaks. Gerrit (tip3p_flex for instance, by skinne

[gmx-users] Re: gmx-users Digest, Vol 65, Issue 83 6. EVB and mapping potentials (rsf)

2009-09-24 Thread Gerrit Groenhof
Hi, I think that you could use the free energy parts of gromacs for your purposes. V1 and V2 can be coupled via a parameter lambda, such that (assuming you're not changing masses/atoms) H(p,r,lambda) = (1-lambda)* V(A-B + C) + lambda*V(A + B-C). IN the manual it is described how to inform gromac

[gmx-users] Re: 3 covalent bonds protein- heme (malve...@iq.usp.br)

2009-09-17 Thread Gerrit Groenhof
/lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 65, Issue 96 * -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.

[gmx-users] Re: gmx-users Digest, Vol 64, Issue 17

2009-08-05 Thread Gerrit Groenhof
THere is documentation available in the manual and at wwwuser.gwdg.de/~ggroenh/qmmm.html If you need a SP computation, do a zero-step MD run: nsteps=0 Frequencies can only be computed numerically I think, but I never tried this. Best, Gerrit >7. QMMM settings (ilona.bal...@bioquant.uni-heid

[gmx-users] Re: gmx-users Digest, Vol 62, Issue 68

2009-06-14 Thread Gerrit Groenhof
requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Di

[gmx-users] Re: Alternative TRP residue

2009-06-11 Thread Gerrit Groenhof
4/attachment.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Dig

Re: [gmx-users] How to obtain a approperiate PDB file of DNA?

2009-04-09 Thread Gerrit Groenhof
ers mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 60, Issue 65 ***** -- Gerrit Groenhof MPI biophysical chemist

[gmx-users] Re: gmx-users] Mopac7 / Gromacs 4.0.4 Issue

2009-04-08 Thread Gerrit Groenhof
Hi, it should suffice to set the LIBS prior to compiling. With what compiler was mopac7 compiled? I have thus far only been able to compile a working version with f2c/gcc. Not optimal. Using the intel fortran compiler, I also get a running mopac, but the results are not correct and I don't

[gmx-users] open positions

2009-03-16 Thread Gerrit Groenhof
antum chemistry, molecular dynamics, and/or computer programming would be great. If you are interested in joining our group, please send a short motivation letter and a cv with contact details of one or two references, preferably by email, to ggro...@gwdg.de. Kind regards, Gerrit -- Gerrit Gro

[gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)

2009-03-06 Thread Gerrit Groenhof
Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each other. The bonds prevent these atoms to get apart too far, so 1-4 won't destabilize the overall structure. The SR part is negative, thus keeping your protein together. Gerrit Message: 3 Date: Fri, 6 Mar 2009 19:43:19 +090

Subject: [gmx-users] gromacs QM/MM

2009-02-18 Thread Gerrit Groenhof
Although there is not much interface specific information, you can check one of our recent papers, eg. L.V. Schaefer et al., PLoS computational biology, 4 (2008), e134. More information on how to build up the interface on the gaussian side you find on wwwuser.gwdg.de/~ggroenh Gerrit -

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin

2008-12-15 Thread Gerrit Groenhof
Saindo do diretório `/usr/local/gromacs-4.0.2/src' make[1]: ** [all] Erro 2 make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src' make: ** [all-recursive] Erro 1 --- I tried it with both Gromacs 4.0.2 and 3.3.3, and the same output error appears; so, probably, it's something

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with, MOPAC7 QM/MM

2008-12-12 Thread Gerrit Groenhof
.f" place: should them stay in the MOPAC folder with files and objects (mopac7-1.10/src) or in LINUX folder with library files (usr/local/lib/)? Laércio Message: 2 Date: Thu, 11 Dec 2008 14:51:34 +0100 From: Gerrit Groenhof Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 wit

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin)

2008-12-11 Thread Gerrit Groenhof
Today's Topics: Well, I removed that line, and "make" gone further, but I stopped in other error: --- make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/kernel' /bin/sh ../../libtool --tag=CC  --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused

[gmx-users] Re: gmx-users Digest, Vol 53, Issue 140: uniform neutralizing plasma for PME (himanshu khandelia)

2008-09-29 Thread Gerrit Groenhof
Type: text/plain; charset="iso-8859-1" Is there an implementation in gromacs for using a uniform neutralizing plasma with PME, to avoid use of counterions? Thank you -Himanshu Neutralization is done implicitly, by omitting out the zeroth plane wavevector (m=0, see sec. 4.6 of the gmx m

Re: [gmx-users] CPMD- QM MM simulation

2008-09-08 Thread Gerrit Groenhof
Message: 1 Date: Fri, 5 Sep 2008 15:48:12 -0700 From: "Chih-Ying Lin" <[EMAIL PROTECTED]> Subject: [gmx-users] CPMD- QM MM simulation To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi I read some papers, which the authors use CPMD

[gmx-users] compilation problem with mopac in gromacs 3.3.3, and x86_64 machine

2008-07-08 Thread Gerrit Groenhof
Message: 1 Date: Tue, 8 Jul 2008 10:18:30 + From: Abu Naser <[EMAIL PROTECTED]> Subject: [gmx-users] compilation problem with mopac in gromacs 3.3.3 and x86_64 machine To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi Gerrit, I am having pr

[gmx-users] Re: QMMM memory problem

2008-07-04 Thread Gerrit Groenhof
Was gromacs configured with the --with-qmmm-gaussian option? Is gaussian installed and running as well? can you make a tar file of the input files (topology, index, mdp, configuration) and send it directly to me (i.e not via userlist)? Gerrit -- Message: 2 Dat

[gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)

2008-06-16 Thread Gerrit Groenhof
Looks like hysteresis. Do you do slow growth, or discrete FEP? Gerrit Dear all Gmxers, I am calculating a mutation free energy from L<->A for a five AA peptides using G96 53a6 force field. however, my dG_for and dG_rev is quite different. dG_for(lambda=0.00) = - 9.9 kJ/mol dG_rev(lambda=1.

Re: [gmx-users] QM/MM compilation

2008-05-21 Thread Gerrit Groenhof
Message: 3 Date: Tue, 20 May 2008 18:59:58 +0200 From: Ran Friedman <[EMAIL PROTECTED]> Subject: Re: [gmx-users] QM/MM compilation To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Dear Gerrit, Hitch-hiking with a related issue.

Re: [gmx-users] atomname -> atomic number

2008-05-14 Thread Gerrit Groenhof
Hi, I would like to write a reader for *.gro files, but I couldn't find any information about how to map the atomname to the atomic number. Can anyone shed some light on this problem? I would be most grateful. The ff*nb.itp file contains already the atomic numbers of the atoms. Probably n

Re: [gmx-users] Avoiding parameterization step

2008-03-11 Thread Gerrit Groenhof
Thank you very much for your response. I am at the moment interested in doing conformational search. Using freeze groups in combination with conformational search does not seem optimal... Is there any good paper that explain nicely about doing the charge distribution calculation? Y

Re: [gmx-users] Avoiding parameterization step

2008-03-11 Thread Gerrit Groenhof
Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. Depends on what you want to do. You most likely would still need the charge distribution, which is the most difficult part of the parametrization part usually

[gmx-users] Re: gmx-users Digest, Vol 43, Issue 49

2007-11-14 Thread Gerrit Groenhof
What you want to do, a dynamic updating of the QM atoms is not implemented yet. The difficulty with such scheme is energy conservation and force conservation when translocating an atom from the MM into the QM region and vice versa. This is a difficult problem. However, there soluitons, see for

[gmx-users] Re: mopac gcc g77 and x86_64

2007-10-30 Thread Gerrit Groenhof
users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 42, Issue 102 ** -- Gerrit Groenhof MPI for Biophysical Chemistry Am

[gmx-users] Re: gmx-users Digest, Vol 41, Issue 10: How to run ED with position restrain along first principle, component (Anirban Ghosh)

2007-09-05 Thread Gerrit Groenhof
4. How to run ED with position restrain along first principle component (Anirban Ghosh) You can either keep it fixed with the -linfix option of mk_edi. The other option is to use the flooding code, with a harmonic restraint on the eigenvector. Check the paper Flooding in groma

[gmx-users] Re: gmx-users Digest, Vol 41, Issue 5: interaction lists in idef.h ([EMAIL PROTECTED])

2007-09-04 Thread Gerrit Groenhof
8. interaction lists in idef.h ([EMAIL PROTECTED]) Dear Will, Have a look at http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/gromacs_I.pdf In idef there is the ilist array, with an element for each of the F_NRE interaction types. THis list is an 1D array of 1D ar

Re:[gmx-users] GAMESS-US for Hybrid QM/MM ( gmx-users Digest, Vol 39, Issue 71 )

2007-07-19 Thread Gerrit Groenhof
Hi All Is there any way to use gamess-us for Hybrid QM/MM calculation with Gromacs instead of using CPMD, GAMESS-uk or gaussion? Not yet, but feel free to write the interface code. I can help you link it all up once an interface code exists. You can either start from mdlib/qm

Re: [Fwd: Re: [gmx-users] QMMM free energy]

2007-05-31 Thread Gerrit Groenhof
Hi Fiske, From what I understand, you want to compute the free energy for changing one or more atoms in the QM subsystem. I never considered doing this because I do not expect to get sufficient sampling. But in my opinion this should be possible. In case only atoms in the QM subsystem change

Re: [gmx-users] QMMM gromacs/CPMD

2006-11-03 Thread Gerrit Groenhof
(1) For QM/MM, even simple QM solute in a MM solvent, Lennard Jones parameters are required to compute the Van der Waals interactions between the QM and MM subsystems. Thus one always needs to give the atoms types for the atoms in the QM system. A simple topology file will do, containing only

Re: [gmx-users] qm_mopac.c problems in building of 3.3.1

2006-10-07 Thread Gerrit Groenhof
Hi Jake, Did you add to the mopac library the gmxmop.o, and dcart.o (http://rugmd4.chem.rug.nl/~groenhof/qmmm.html#code) before linking to gromacs? The functions domldt and domop are in gmxmop. Gerrit On Oct 6, 2006, at 8:41 PM, Jake Michaelson wrote: Hi all, I'm trying to build a qmmm

Re: [gmx-users] QMMM interface

2006-09-28 Thread Gerrit Groenhof
It does not exist, but since gmx is open source, I suggest you give it a try. I suppose the input/output is similar to gamess-uk? In that case, have a look at mdlib/qmmm.c and gamess.c. Contact me off list at ggroenh<>gwdg.de if you need more help. Gerrit On Sep 28, 2006, at 3:01 PM, [EMAIL

Re: [gmx-users] How can I remove water and ion molecules

2006-09-25 Thread Gerrit Groenhof
make an index file entry with the stuff you want to write in your pdb, and use editconf -n to dump only that. On Sep 25, 2006, at 5:05 PM, Guillem Portella wrote: man grep with special attention to -v option bounus ball: it also works before em and md Cheers On Monday 25 September 2006

Re: [gmx-users] vacuum simulation problem

2006-08-09 Thread Gerrit Groenhof (RUG)
In addition to Erik and my suggestions, you should also remove the overall rotation: comm_mode=linear. [EMAIL PROTECTED] wrote: Dear all, I am simulating a protein containing 2 domains which are linked together by a loop of around 10 residues. When I am simulating the same in vacuum, after a

Re: [gmx-users] Vacuum simulation problem

2006-08-09 Thread Gerrit Groenhof (RUG)
Do not use Pressure coupling in vacuo. ALso you seem to be running with periodic boundary conditions. Switch that off as well and use ns_type = simple, and finally use infinite cut-offs when simulating in vacuo. qa cut-off of 0.9 is way too short. If you think the lack of water causes the confo

Re: [gmx-users] simulation at particular pH

2006-08-08 Thread Gerrit Groenhof
Bad idea. Adding just one proton (1/Navogadro moles ~ 1.6 * 10^-24)to a box of say 500 nm^3 (5 10^-22 liter), continaining roughly 1 waters would give a pH of 2.5 (-log[1.6/5*10^-2), which is the maximum pH you can reach for such standard box. If you want to go higher, say to pH=7, your bo

Re: [gmx-users] what is "MPI process rank 0 (n0, p18041) caught a SIGSEGV"

2006-08-07 Thread Gerrit Groenhof (RUG)
Recompile the mopac library with larger arrays. You can set these in the SIZES file in the mopac sourcedir (MAXORB). Do not forget to recompile also mdrun afterwards,as the library (.a) will be statically linked. Gerrit Mahnam wrote: In God We Trust Hello GMX users I want to do QM/MM by G

Re: [gmx-users] PME usage in 3.3 & g_energy: doubt ?

2006-08-01 Thread Gerrit Groenhof (RUG)
First, with rlist = rvdw, you will not get long range Lennard Jones interactions. In fact I would recommend using a larger vdw cut-off, as 0.9 is very short. Are you sure you are using the same mdp file? About the LR coulomb, it will only appear if you have rlist < rcoulomb. In that case the s

Re: [gmx-users] langevin dynamics

2006-07-31 Thread Gerrit Groenhof (RUG)
I think you do not use the bd_fric in combination with sd, but with bd, the friction is set by the tau_t instead. Did you als use different parameters for that? For bd, you would use the friction bd_fric to set the ld friction, but not for sd, but I could be wrong here... Gerrit syma wrote:

Re: [gmx-users] does gromos force field can explain pi-pi interaction

2006-07-27 Thread Gerrit Groenhof (RUG)
The most recent paper I read on this is by Piacenza and Grimme (J. AM. CHEM. SOC. 2005, 127, 14841-14848 ). They use a very efficient DFT based approach with an empirical correction to compute accurate stacking energies. At least so they say. Unfortunately their method DFT-D is not yet availab