Re: [gmx-users] Population Density Plot

that can perform that task, I just felt it was important to underline that a kernel density estimation is what is needed in this case. If you go back to your original reply, there's nothing in there that can help the original poster solving his problem. J On Mon, Sep 17, 2018 at 3:43 PM Vytautas

Re: [gmx-users] Population Density Plot

Also you can use R for that task. Very easy like:density(x, ...) On Monday, September 17, 2018, 4:26:38 PM GMT+3, João Henriques wrote: How does that reply the OP's question? To calculate the joint probability distribution you need to perform a kernel density estimation. I'd recommend

Re: [gmx-users] Population Density Plot

Gromacs xvg files can be opened with Xmgrace and you should get plot out of them right away then. I am not sure that those plots fit your need but you can edit them with same program right away.Xmgrace is probably available over your Linux distribution package manager like "sudo apt-get

Re: [gmx-users] Error in NVT equilibration

And what about OPLS-AA/L if I do nvt equilibration of my protein in water with it is it OK to do constraints = all-bondsall the time like I am used to do? On Monday, September 17, 2018, 3:18:51 PM GMT+3, Justin Lemkul wrote: On 9/17/18 8:12 AM, Vytautas Rakeviius

Re: [gmx-users] Error in NVT equilibration

Can you explain more to us when it is not appropriate to constrain all bonds during nvt equilibration? On Monday, September 17, 2018, 3:06:56 PM GMT+3, Justin Lemkul wrote: On 9/17/18 8:04 AM, Vytautas Rakeviius wrote: >  I think your attachment to email was lost during re-trans

Re: [gmx-users] Error in NVT equilibration

I think your attachment to email was lost during re-transfer and it would be nice to see that, but I think what you need is:constraints= all-bondsIn that mdp file. On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, Cristina wrote: Dear Gromacs

Re: [gmx-users] Regarding index .ndx files

Without going into details and setting: tc-grps = System should allow to proceed without fatal errors. On Monday, September 17, 2018, 1:58:50 PM GMT+3, Sebastian Muraru wrote: Hi there! I am a Masters student and this is my first email to the list. I would just like to ask whether

Re: [gmx-users] (no subject)

I suggest this tool:https://github.com/llazzaro/acpype On Friday, September 14, 2018, 10:44:56 PM GMT+3, SAKO MIRZAIE wrote: Hi every one, I need the topology parameters for pyridoxal phosphate linked to lysine with amber99sb force field. does anyone have the mentioned parameters? I

Re: [gmx-users] lie calculations

Hi I think you should check this paper:Åqvist J, Medina C, Samuelsson JE. A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, Design and Selection. 1994 Mar 1;7(3):385-91.It explains everything and gives example of use.And yes with different water

Re: [gmx-users] charmm2gromacs.py

I never tried that myself, but I think you such check this:J. Chem. Inf. Model., 2016, 56 (6), pp 1112–1116DOI: 10.1021/acs.jcim.6b00103 On Wednesday, September 12, 2018, 11:19:44 AM GMT+3, Frederic Schneider wrote: Hi, i use the parameter generator for organic molecules at

Re: [gmx-users] core-dumped

Investigate atoms 18720 and 18723 mentioned in error. From my experience such error happens when two atoms collide in completely unrealistic fashion.This error also dumps some pdb files at exact moment when things went really wrong and that ones you should look at. Also I do not know what kind

Re: [gmx-users] Help

https://www.urbandictionary.com/define.php?term=btw :) He wants you to try never version 2018.2: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz Also try different fftw options. On cmake line add: -DGMX_FFT_LIBRARY=xxx where xxx can be fftw, mkl or fftpack. You also need proper stuff

[gmx-users] gmx genion -neutral adds some opposite charge under some conditions

Hi, My system has non-zero total charge: 34.09. I do gmx genion -neutral on it, I get 35 CL ions dumped into it. So I continue to get warning "System has non-zero total charge: -0.91". Fell free to try with your own system. I think this should be fixed. -- Gromacs Users mailing list *

Re: [gmx-users] S-nitrosoylated proteins

I suggest to check this one: Han S. Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin. Biochem Biophys Res Commun. 2008 Dec 12;377(2):612-616. doi: 10.1016/j.bbrc.2008.10.017. Epub 2008 Oct 16. PubMed PMID: 18929538. On Wednesday,

Re: [gmx-users] Deuterium atoms

Just change all D to H in structure file IMHO. On Wednesday, June 20, 2018, 5:39:18 PM GMT+3, Hermann, Johannes wrote: Dear all, is there any force field in gromacs (or elsewhere) which can handle deuterium atoms? All the best Johannes -- __

Re: [gmx-users] (no subject)

Also depends on what you try to do. Maybe Dry Martini? Look into:ARNAREZ, Clément, et al. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. Journal of chemical theory and computation, 2014, 11.1: 260-275. On Thursday, June 21, 2018, 5:22:15

Re: [gmx-users] md simulation of oil hydrocarbon

I think you should check as others did ex.: Optimization of the OPLS-AA Force Field for Long Hydrocarbons J. Chem. Theory Comput., 2012, 8 (4), pp 1459–1470   On Monday, May 28, 2018, 8:23:50 PM GMT+3, Atila Petrosian wrote: Hi all, I want to do md simulation of oil hydrocarbon? Is

Re: [gmx-users] installing Gromacs on windows using cygwin

If you use bash just add source /usr/local/gromacs/bin/GMXRC to ~/.bashrc file as separate line, like: echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc or just use your favorite text editor. On Monday, April 23, 2018, 1:57:02 PM GMT+3, Hossein Geraili wrote:

Re: [gmx-users] (no subject)

You should give more details how you try to make residue 44 immobile. Keep in mind that some ways to do that can be "defeated" with strong enough pulling. Most likely you just have to try few times with different pulling and restraining options. On Tuesday, January 2, 2018, 12:30:59 PM

Re: [gmx-users] DSSP

ftp://ftp.cmbi.ru.nl/pub/software/dssp/ There you can find windows .exe version of it. On Tuesday, December 5, 2017, 7:38:44 AM GMT+2, Vidya R wrote: Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install

Re: [gmx-users] water molecule cannot be settled during minimization!!!!

Investigate same water molecule mentioned in error in vmd or such program likely it is in close contact to other molecule.You can move it manually by altering coordinates in gro text file into more realistic starting position.Or probably even better if you redo your solvatation again (with

Re: [gmx-users] pdb (CTAB) into .GRO

It seems that ctab.pdb contains residue 'XXX'. Verify that with pdb viewer such as pymol etc. Residue 'XXX' is not standard amino acid with 3 letter code so in lead to such error.Maybe you can delete it with same pdb viewer, or fix that naming error somehow. Its up to you to decide. On

Re: [gmx-users] force field for selinomethionine?

As far as I see others just replace selenium with sulphur, convert of selenomethionine to methionine like:https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-775 On Wednesday, November 1, 2017, 8:24:10 AM GMT+2, Seera Suryanarayana wrote: Dear

Re: [gmx-users] itp file for aminoacids

Generally you do not need such thing as parameters for amino acids come from force filed itself together with Gromacs.It you still want to make one just check scientific papers how force fields were created. On Monday, October 30, 2017, 4:41:50 PM GMT+2, rose rahmani

Re: [gmx-users] where can i find .itp file for amino acids?

Maybe just rename your custom thr.itp THR and in other places to something else to avoid conflict with default version?amber03.ff is in gromacs-version/share/top folder. There you can find aminoacids files with default amber03 THR. On Saturday, October 28, 2017, 3:54:41 PM GMT+3, rose

Re: [gmx-users] Number of coordinates in .gro file does not match topology

You do something wrong. How you solvate?Try something like this: gmx solvate -cp my_system.gro -cs spc216.gro -o my_system_solv.gro -p topol.top On Monday, October 30, 2017, 10:41:31 AM GMT+2, Aishwarya Smriti wrote: Hi! I'm trying to solvate a system of

Re: [gmx-users] Gromacs error

You really need cuda? IF no you can try:cmake .. -DGMX_GPU=OFF On Sunday, October 29, 2017, 7:26:04 AM GMT+2, Kunal Dutta wrote: Hi, I have the following problems kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..

Re: [gmx-users] Potassium channel EM Segmentation fault

I suggest ignoring/deleting TL and then replacing waters with K randomly with:gmx genion.Ofc. it depends what you try to do. On Wednesday, October 11, 2017, 5:01:52 PM GMT+3, Du, Yu wrote: Dear GMX Users, Keyword: metal, energy minimization, segmentation fault

Re: [gmx-users] problem of GB simulation

Most likely you do something wrong in energy minimization step: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.htmlMake sure you produce plot similar like in that page with your system before proceeding further with minimized system. On

Re: [gmx-users] purpose of step pdb files during MD

Energy minimization output explains them. I do not think they are important if you get good energy minimization after all. On Thursday, September 7, 2017, 3:41:59 AM GMT+3, Vedat Durmaz wrote: hi guys, from time to time i'm faced with GMX output files during MD

Re: [gmx-users] Error while running perl distances.pl

6-791, Korea  Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850 Email: f07...@kist.re.kr         -------Original message--- From: "Vytautas Rakeviius "<vytautas1...@yahoo.com> To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장

Re: [gmx-users] Error while running perl distances.pl

Script assumes that variable $distance is the second row separated by space in the file dist{number}.xvg which appears after execution of system call gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'I just

Re: [gmx-users] g_mmpbsa compilation error

Likely you cmake is far newer than Gromacs (cmake --version to figure that out). You should try Gromacs 2016.3 On Friday, September 1, 2017, 12:55:14 PM GMT+3, neha chaudhary wrote: Hi, I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS

Re: [gmx-users] Gromacs simulation of two or more peptide chain

Generally that means you starting system is seriously wrong. Investigate atom 218 and surrounding area. Another atom really close or sth like that. On Thursday, August 24, 2017, 9:36:37 PM GMT+3, Kalyanashis Jana wrote: Dear all, I would like to run an MD simulation

Re: [gmx-users] Trouble with gmx distance

Two atoms for distance calculation have to be in same selection thus program expects even number of positions and do not get in my opinion.You could show your index.ndx for better investigation. On Monday, August 21, 2017, 9:24:35 PM GMT+3, Sotirios Dionysios I. Papadatos

Re: [gmx-users] gromacs error

Make sure you have libfftw3f installed properly. In such case command:whereis libfftw3fshould give you location of that file which gmx is unable to find. On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta wrote: Hi gromacs users, How to fix this error? gmx:

Re: [gmx-users] Unable to install 5.1.14

You have updated boost so you have to update GROMACS too. 2016.3 is the latest version you should download it. Another possibility is to downgrade boost to older, but you can bump into other mish-mash issues. I do not recommend that. On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat

Re: [gmx-users] GROMACS with Torque: Job stuck

Check log files in server_logs and mom_logs folders in the TORQUE_HOME. You can find there what is going on in more detail. On Friday, August 25, 2017, 4:25:03 PM GMT+3, Souparno Adhikary wrote: Hi, This is related to running GROMACS through mpirun and Torque. After

Re: [gmx-users] gmx distance

Enter both groups into one line. On Friday, August 25, 2017, 2:43:47 PM GMT+3, Sergio Manzetti wrote: Hello, I am trying to find the average distance between two groups in a trajectory, defined by the index.ndx file and the traj.xtc, the options are

Re: [gmx-users] installation_server machine_error

Well it seams that you compiled Gromacs with mpi support so now you should run it with sth. like that: mpirun -np 1 /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx_mpi -f 1aki.pdb -o 1AKI_processed.gro -water spceRun:man mpirunfor more details. On Wednesday, August 23, 2017, 10:42:47 AM GMT+3, Kashif

Re: [gmx-users] use INTERFACE Force Field

Hello, Possible bot not easy.Look into Gromacs folder share/top/ all force fields sit there as text files your will have to make ITERFACE text files in same format and layout.What you download as ITERFACE force field are also text files with parameters, but layout is for different programs.

Re: [gmx-users] Simulations stop running after reaching specific time step

Maybe post your mdp file. There are settings about writing out and default values if you add nothing too. On Tuesday, June 27, 2017 10:44 AM, Shobha Sharma wrote: Hello, I am submitting few simulations, after providing the wall time enough to finish the

[gmx-users] Adding multiple different ligands with acpype

Hello, I try to add multiple and different ligands with acpype and bump into issue "Invalid order for directive atomtypes" discussed before (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-July/035223.html)I can comment out other ligands leaving one and then it seems OK. I do

Re: [gmx-users] error in running md

Check structure, mainly atom numbers given in messages. Bad contacts or something. On Tuesday, June 13, 2017 1:45 PM, VARSHA RANI wrote: Hi, I ran minim.mdp for my system with 3456 atoms.  But lowest energy after minimization is positive. *here is th screen

Re: [gmx-users] gromacs-5.1.4 installation issue

This kind of issues can mean that you moved compiled binary to quite different machine. Though I am not sure what you did. Compile on the same machine you are going to use or at least as similar as possible (same Linux ver. with same updates). On Wednesday, May 24, 2017 3:13 PM, abhisek

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

getting the same error. > > Regards, > Steffen > > Date: Wed, 24 May 2017 08:45:57 + (UTC) > > > From: Vytautas Rakeviius <vytautas1...@yahoo.com> > > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>, > >      "gromacs.org_gmx-users@m

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Ubuntu 17.04 should give you quite up-to date gcc and co. Make sure you try this on clean folder: remove everything download and try again. Maybe some old files interfering. On Wednesday, May 24, 2017 4:14 AM, Steffen Graether wrote: Hi, I’ve tried installing

Re: [gmx-users] User Defined Potentials

Inside GROMACS folder go share/top/ you will find folders for force fileds like gromos53a5.ff/ there are files with water topology like tip3p.itp you can write your own using them as examples. On Tuesday, April 25, 2017 12:58 AM, Ommair Ishaque wrote: Hi, I am Phd

Re: [gmx-users] make

Its stated in:"GNU version! gcc versions later than 5 are not supported!"The most simple solution is just download newer GROMACS version like 2016.3. On Thursday, April 20, 2017 1:53 PM, Anshul Lahariya wrote: hello, i am a new user installing gromacs on

Re: [gmx-users] Gromacs - MD run

Selected force field determines what will be pushed and what will be pulled during MD run. Which one you use? Maybe just try other. On Thursday, April 20, 2017 1:20 PM, Mariusz Wierzbowski wrote: Dear Gromacs users, I am not sure what is the problem with my

Re: [gmx-users] Gcc

Its quite problematic to alter existing Linux install in such way and better download proper gromacs version or such.Another possibility just select appropriate Linux distribution and version ex. my Slackware 14.2 comes with gcc 5.3.0. On Thursday, April 20, 2017 1:42 PM, Anshul Lahariya

Re: [gmx-users] PROTEIN FOLDING

Yes, you can open all structural output files with VMD. Or Chimera (tools MD so on). On Thursday, April 6, 2017 9:56 AM, Neha Gupta wrote: Hi gromacs users, I have run 2ns simulation of protein ligand complex using NVT ensemble (after equilibration). I

[gmx-users] Building box arround given membrane with gmx solvate. As small as possible.

Hello, I want to build box around my membrane with gmx solvate or sth. Ofc. I do not want water in side gap between membrane and box. I do like this: gmx editconf -f gap_processed.gro -o gap_newbox.gro -c -bt cubicI expect -d 0 so everything packed in box as tightly as possible, but still after

Re: [gmx-users] how to know solvent molecule number

Oh sorry number of atoms you will have to divide by number of atoms in ethanolamine. On Wednesday, April 5, 2017 4:45 PM, Vytautas Rakeviius <vytautas1...@yahoo.com> wrote: head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. Solvate then do same on new file

Re: [gmx-users] how to know solvent molecule number

head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. Solvate then do same on new file: head -n 2 obj_solv.gro | tail -n 1All you need is difference. On Wednesday, April 5, 2017 4:13 PM, Chintan Bhagat wrote: Hello, I want to do stimulation

Re: [gmx-users] gmx mdrun

"my CPU switches off automatically"? Can you expain what actually happens. Windows go to sleep etc?Also you should do such things on Linux, cygwin is not that fast as you see in warning message. On Sunday, April 2, 2017 11:24 AM, Neha Gupta wrote: Hi gromacs

Re: [gmx-users] (no subject)

You can use acpype to prepare ligands for MD run. On Wednesday, April 5, 2017 1:01 PM, maria khan wrote: Dear Erik.. I have studied the manuals of gromacs and from that i came to know that gromacs use united atom ff thats why i asked and in manuals many

Re: [gmx-users] CHARMM27 hates my DMPC

-ignhI get error about hydrogen which I try to ignore. Very strange for me. -ignh option is not possible with CHARMM ff? On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 4/4/17 8:52 AM, Vytautas Rakeviius wrote: > Hello, > I have my syst

[gmx-users] CHARMM27 hates my DMPC

Hello, I have my system with DMPC bilayers in pdb and try to convert it into GROMACS input. Because system is with lipids I think chose CHARMM27 ff. But still I get lots of warnings like that: https://pastebin.com/K8dHKkUi Also I add my DMPC pdb as example. What should I do? Rename all my DMPC

Re: [gmx-users] Energy Miinimization question

As you set smaller emtol you do better and longer minimization. So with 1000 you stop simulation way before polymer forms some rings. You can check video with VMD Chimera or something. On Saturday, April 1, 2017 8:25 PM, Mishelle Oña wrote: Hello everybody, I

Re: [gmx-users] Regarding structure conformation

MD can not simulate chemical reactions. What you can do prepare different forms with acpype and compare all in some way. On Monday, April 3, 2017 6:51 AM, Dilip H N wrote: Hello, I have a non zwitterionic glycine molecule, and have solvated it with water,

Re: [gmx-users] FAD parameters in CHRAMm36 ff

I think you should use cgenff for FAD in such case. They are compatible and can by used together. On Friday, March 31, 2017 9:29 AM, Amir Zeb wrote: Hello Folks, I want to simulate a protein where FAD is included as co-factor. I will use CHARMm36 ff but I don't

Re: [gmx-users] Pull Code constant value

I suggest trial and error in quite short runs without wasting time on waiting for next day or so. Really large k can create segmentation faults or "cannonball into wall" like effects in MD movie. On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary wrote: Hi

Re: [gmx-users] Regarding structure

If you interested in just one glycine one possible solution is to prepare it with acpype instead. It respects your hydrogens and you can set charge as command line option. On Friday, March 24, 2017 6:14 AM, Jonathan Saboury wrote: Please be considerate to others

[gmx-users] g_membed or alternative on GROMACS 2016

Hello, I am reading "Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail" ( http://dx.doi.org/10.1016/j.bpj.2011.06.010) and it mentions tool called: g_membed but I can not find it on recent GROMACS 2016 versions. It was removed

Re: [gmx-users] COEFFICIENT FOR LINEAR INTERACTION ENERGY IN PROTEIN LIGAND COMPLEX

Hello, Here one recent paper with new parameters for LIE derived:https://www.ncbi.nlm.nih.gov/pubmed/26373640You just extract energy terms and then do some MLR fitting with R or something. Maybe even recent version of MS Excel can do this. On Thursday, March 23, 2017 7:24 AM, Neha

Re: [gmx-users] Error in free energy calculation

As article name in reference says PLUMED can be used for free-energy calculations with molecular dynamics. On Thursday, March 16, 2017 1:23 PM, Hannes Loeffler <hannes.loeff...@stfc.ac.uk> wrote: On Thu, 16 Mar 2017 10:09:58 + Vytautas Rakeviius <vytautas1...@yahoo.c

Re: [gmx-users] LINEAR INTERACTION ENERGY

; in mdp file Could you please say more about it? Thanks, Kulkarni.R From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Vytautas Rakeviius <vytautas1...@yahoo.com> Se

Re: [gmx-users] LINEAR INTERACTION ENERGY

Basically you do two MD runs one with ligand in water other with ligand in protein. You must set proper energygrps in mdp file so you get 2 edr files from runs and in the end you use "gmx lie" (http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between those two edr

Re: [gmx-users] Error in free energy calculation

You should try to add PLUMED (plumed.org) to GROMACS for such things.Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., ... & Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications,

Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

/ruaxx6nbj2qpvm6/MD_4AK0_test_pub.tar.bz2 How can I drag 195 and 281closer with distance restraints? (not necessary as close as 0.2 nm) On Wednesday, March 15, 2017 2:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/15/17 6:28 AM, Vytautas Rakeviius wrote: > Hello, I try to add

[gmx-users] Distance restraints on two TYR OH groups so that they are together

Hello, I try to add distance restraints on two TYR OH groups so that they are together in the end like this: [ distance_restraints ]  195 281 1 1 1 0.2 0.22 0.24 1000 But it does not work at least over time frame I tested, they even go further away from each other. Here I share my all

Re: [gmx-users] I want to drag two atoms together with GROMCS SMD options.

Thanks, and now after some time I get:"Pull reference distance for coordinate 3 () needs to be non-negative"How to solve this error? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] I want to drag two atoms together with GROMCS SMD options.

Hello, I want to drag two atoms together with GROMCS SMD options.But I tried different options and still those groups are pushed away one from another.I would be very thankful if someone edits this code example (from:

[gmx-users] Errors There were 2 inconsistent shifts. Check your topology after I moved my peptide with VMD

Hello, I used my charmm-gui.org built system on Gromacs for some time. Then I tried to adjust it little bit and moved my peptide with VMD to other place. I am not sure it is fine because I can get clashes and so on, but I tried it. I want to reuse same topology. Now try to minimize it again and

[gmx-users] ftp.gromacs.org not working now

I need this file: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gzthx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Minimisation failure: The charge group moved more than the distance allowed by the domain decomposition

Here all my files: https://www.dropbox.com/s/94u9b9stsk84ckz/1oyn6wat1994-15a_vconf-docking_1.tar.bz2 I try minimize this with: grompp_mpi_d -maxwarn 2 -f ~/emamber.mdp -c *_solvated_bonded_GMX.gro -p *_solvated_bonded_GMX.top -o em.tpr mdrun_mpi_d -deffnm em Here is my emamber.mdp file: