[gmx-users] help for debye waller factor calcuations
Dear all, I am trying to calculate mean square relative displacement (MSRD), debye-waller factor, of single or multiple scattering of EXAFS spectra. Can any expert introduce how to calculate them using gromacs tools or some other tools? Any help is appreciated. Best, Shaofeng Wang Ph.D Email: wangshaof...@iae.ac.cn Key Laboratory of Pollution Ecology and Environmental Engineering Institute of Applied Ecology Chinese Academy of Sciences China -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to use "echo" to output index file with only one command line?
You need to include the newlines in your echo to get the result you want. Cheers On Sun, 10 Feb 2019, 22:38 ZHANG Cheng <272699...@qq.com wrote: > I can successfully output the index file by doing it step by step: > > > $ gmx make_ndx -f equilibration.gro > $ r 1-442 > $ q > > > But I am not sure how to do it in just one line. > > > I tried these but all could not work > > > $ echo r 1-442 q | gmx make_ndx -f equilibration.gro > $ echo "r 1-442" q | gmx make_ndx -f equilibration.gro > $ echo "r 1-442" "q" | gmx make_ndx -f equilibration.gro > > > Thank you! > -- > 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 (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to use "echo" to output index file with only one command line?
I can successfully output the index file by doing it step by step: $ gmx make_ndx -f equilibration.gro $ r 1-442 $ q But I am not sure how to do it in just one line. I tried these but all could not work $ echo r 1-442 q | gmx make_ndx -f equilibration.gro $ echo "r 1-442" q | gmx make_ndx -f equilibration.gro $ echo "r 1-442" "q" | gmx make_ndx -f equilibration.gro Thank you! -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with extending simulation with checkpoint files after running from parent directory
Hello,
I have looked for a solution for my problem in the old messages but I
haven't been able to find it.
I ran a script in a parent directory to run simulations in many inner
directories, placing the outputs in the corresponding directories. Now that
I want to extend these simulations I am trying to do this with the last
checkpoint files. However, when I try to do this for the first inner
directory ("monolayer05") I get this error:
"Output file appending has been requested,
but some output files listed in the checkpoint file
monolayer05/checkpointrun1_05.cpt
are not present or not named as the output files by the current program:
Expect output files present:
Expected output files not present or named differently:
monolayer05/step8_0_1_newtemp05.log
monolayer05/step8_0_1_newtemp05.trr
monolayer05/step8_0_1_newtemp05.edr"
I guess the checkpoint file has been written weirdly since I outputted it
from the upper directory. The .log, .trr, and .edr are all in the
monolayer05 directory, but the program can't seem to find them. I have
tried creating another directory called monolayer05 within monolayer05 and
copy the three files in there, but that doesn't work. I have also tried
manually editing the checkpoint file and changing the names to remove the
monolayer05, but then I get a different error about a corrupted or
truncated checkpoint file.
I've been messing with this for a while, and I would really appreciate any
ideas.
Thanks a lot,
Cian
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Re: [gmx-users] (no subject)
http://manual.gromacs.org/documentation/current/reference-manual/topologies/force-field-organization.html FFs are located in the share/gromacs/top directory. If you have your own FF that isn't included in the distribution with GROMACS, you can either add it to that directory, or have the FF directory within the directory you run the simulation. Then you simply refer the links in your topology files to that location. Or are you asking how you can solvate your molecule within ethanol, so you have it located in an ethanol solution, then run the simulation? See http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Sat, 9 Feb 2019 at 05:30, Satya Ranjan Sahoo wrote: > Sir, > Can anyone suggest how I can use ethanol force field to solvate and run MD > for my molecule. Please help. > > On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo wrote: > > > Sir, > > I am a beginner to GROMACS. I was unable to understand how to create all > > the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp , > > nvt.mdp , porse.itp , topol.top input files for molecular simulation of > my > > molecule. Please teach me how can I generate or create all the above > > mentioned input files for my molecule. > > > -- > 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 (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand-polymer interaction in triclinic unit cell
1/ as long as the frame within the .tpr file or first frame within the .xtc file fed to trjconv has the molecules/particles as shown in figure 1, then it should maintain them as such, even if they diffuse away. I'd recheck what you have done there. 2/ periodic_molecules is for molecules that cross the PBC boundary, typically those that are a single long chain that links back to itself at the other end. http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=periodic%20molecules#mdp-periodic-molecules. The box you are visualising doen't actually exist within the simulation, it is an artificial construct so that you can look at it. And you can place that box where ever you like. What is important is the relative positioning of the molecules to each other, and whether that is valid with respect to what you are studying. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 8 Feb 2019 at 11:36, Wei-Ta Li wrote: > Hello everyone, > > I am trying to simulate interaction of polymer with ligand. The polymer is > represented by infinite sheet build by propagation in 2 dimensions of > monomer obtained from crystal structure. Since the polymer was crystallized > in triclinic unit cell, the propagation of the sheet also appears to be > triclinic. The topology was obtained by "gmx x2top ... -pbc". The schematic > representation of the structure before simulation is shown below where the > monomer units are *, L is the ligand, \ are boundaries of the unit cell and > water is omitted for the sake of simplicity: > > \\ > \ \ > \ \ >\ \ > \ L \ > \ \ > \ \ >\**\ > \**\ > \**\ > > System was simulated with typical parameters and "pbc = xyz", > "periodic_molecules = yes" flags. After extraction of trajectory with "gmx > trjconv -s whatever.tpr -f whatever.trr -o whatever.pdb -pbc nojump -dt > 10", the structure looks like scheme below: > > \\ ** > \\ * > \\ >\ \ > \ L\ > \ \ > \ \ >\ \ > \ *\ > \**\ > > From Gromacs manual I understand that such representation is expected > because regardless of the input box shape the simulation proceeds in the > brick-shape form: "Even when simulating using a triclinic box, GROMACS > always keeps the particles in a brick-shaped volume for efficiency, as > illustrated in Fig. 3.1 for a 2-dimensional system". Nonetheless I have 2 > questions: > > 1) Why "-pbc nojump" processing does not result in the representation like > in Scheme_1? Shouldn't it put the atoms back in the original box like > stated in the description: "nojump checks if atoms jump across the box and > then puts them back"? Or does it mean brick-shaped box which Gromacs uses > for simulation? Is there other way to have representation after simulation > as in scheme 1? > > 2) Second question is somewhat naive, but nonetheless. Is such skewed > representation of the polymer sheet valid for simulation set up? In other > words, does this "skewness" have effect on polymer-ligand interaction? In > the brick shaped representation the left side has 3 layers, but the right > is gradual ladder-like increase of layers from 1 to 3, and then there is a > fragment of polymer on top of the box. Does the setting "periodic_molecules > = yes" take care of it? > > Thanks in advance! > Wei-Ta Li > -- > 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 (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 178, Issue 37
Hi Justin, Thank you for the information. This is a bit disheartening: "There is no water model that achieves correct agreement with all structural, dynamic, and thermodynamic properties of water" But, I guess that's what you get with force fields rather than using QM methods. If you have any familiarity with them, do you think any of the reactive force fields are better? (Though even if they are I gather they are about 50X slower, which is essentially intractable for many models) Sincerely, James Ryley, PhD, Patent Agent This communication is confidential and may be subject to legal privilege. Nothing contained herein should be construed as legal or patenting advice. On Sat, Feb 9, 2019 at 1:48 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Do hydrogen bonds innately exist using mdrun? (James) >2. Re: Do hydrogen bonds innately exist using mdrun? (Justin Lemkul) >3. non-bond (Coulomb, van der Waals) interactions scaled down to > 40% of their original value (Jianna Blocchi) >4. Re: Fatal Lambda error (Magnus Lundborg) >5. Simulated Annealing (Shan Jayasinghe) > > > -- > > Message: 1 > Date: Fri, 8 Feb 2019 14:20:27 -0800 > From: James > To: GROMACS Listserv > Subject: [gmx-users] Do hydrogen bonds innately exist using mdrun? > Message-ID: > < > caehcax-tzvt3n8hataaggvznafesd46l+bscrszeuwgbhgv...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > I know that gromacs has an hbond command which will analyze hbonds after a > run. But, during a run, without doing something like specifying partial > charges, do hbonds exist? > > It seems to me that they do not, because if I put two water molecules next > to each other, they do not assume the configuration they would if hbonds > were present, nor do the energies come out as expected (the affinity of the > two water molecules is 10X too low, which makes me think that gromacs is > using VDW, but ignoring hbonds). > > I'd love to be wrong and find out that hbonds "just work"! But, if they do > not "just work," how do you specify them? I could see mimicking them by > tuning partial charges on the donor and acceptor atoms to give the correct > affinity, but it seems like that still would not be accurate because hbonds > are angle dependent, whereas long range non-bonded forces are not. > > Sincerely, > James Ryley, PhD, Patent Agent > > This communication is confidential and may be subject to legal privilege. > Nothing contained herein should be construed as legal or patenting advice. > > > -- > > Message: 2 > Date: Fri, 8 Feb 2019 19:40:05 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Do hydrogen bonds innately exist using mdrun? > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 2/8/19 5:20 PM, James wrote: > > Hi, > > > > I know that gromacs has an hbond command which will analyze hbonds after > a > > run. But, during a run, without doing something like specifying partial > > charges, do hbonds exist? > > > > It seems to me that they do not, because if I put two water molecules > next > > to each other, they do not assume the configuration they would if hbonds > > were present, nor do the energies come out as expected (the affinity of > the > > two water molecules is 10X too low, which makes me think that gromacs is > > using VDW, but ignoring hbonds). > > > > I'd love to be wrong and find out that hbonds "just work"! But, if they > do > > not "just work," how do you specify them? I could see mimicking them by > > tuning partial charges on the donor and acceptor atoms to give the > correct > > affinity, but it seems like that still would not be accurate because > hbonds > > are angle dependent, whereas long range non-bonded forces are not. > > There is no explicit energy function associated with hydrogen bonds. > Many force fields used to include such a term, but it was found to be > unnecessary with better parametrization. Hydrogen bonds arise due to > favorable electrostatic interactions and are entirely a function of the > water topology. Don't mess with topologies, because as you "fix" one > thing, you break a whole host of others. There is no water model that > achieves correct agreement with
[gmx-users] Periodic Boundary Conditions
Hello I want to do noPeriodic Boundary Conditions for my system. Gromacs tutorial has said that it can not be used the center and nojump in one command simultaneously. I would be grateful if you could explain the reasons for it? please see this tutorial http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Thanks a lot. -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to calculate msrd using the tool of gromacs
Dear all,I want to calculate the debye waller factor ( or mean square relative displacement ) of single or multiple scattering of specific path using md configuration. Can some expert introduce how to calculate them using gromacs tools?Any help is appreciate,Best,ShaofengInstitute of applied ecology,CAS-- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fatal Lambda error
Hi, As Magnus hinted, the valid range for i is 0 to 20, so change the bash script so that it does not reach 21. Mark On Sat., 9 Feb. 2019, 10:26 Magnus Lundborg, wrote: > The lambda states are numbered from 0. You only have 21 different states in > your mdp file. Therefore your init-lambda-state can range from 0 to 20. > > Cheers, > > Magnus > > Den fre 8 feb. 2019 23:08 skrev Angelina Malagodi < > angelinamalag...@gmail.com>: > > > Sorry, if the attachments don't load, here are the uploaded texts. > > Thank you once again, > > > > Angelina > > > > > > *Job submission: * > > > > #!/bin/bash > > > > # Set some environment variables > > FREE_ENERGY=`pwd` > > echo "Free energy home directory set to $FREE_ENERGY" > > MDP=$FREE_ENERGY/MDP > > echo ".mdp files are stored in $MDP" > > > > # Change to the location of your GROMACS-2018 installation > > GMX=/usr/local/gromacs/bin > > > > for (( i=0; i<22; i++ )) > > do > > LAMBDA=$i > > > > # A new directory will be created for each value of lambda and > > # at each step in the workflow for maximum organization. > > > > mkdir Lambda_$LAMBDA > > cd Lambda_$LAMBDA > > > > ## > > # ENERGY MINIMIZATION STEEP # > > ## > > echo "Starting minimization for lambda = $LAMBDA..." > > > > mkdir EM > > cd EM > > > > # Iterative calls to grompp and mdrun to run the simulations > > > > $GMX/gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c > > $FREE_ENERGY/curcumin/solv_curenol_54a7.gro -p > > $FREE_ENERGY/curcumin/topol.top -o min$LAMBDA.tpr > > > > $GMX/gmx mdrun -deffnm min$LAMBDA -ntmpi 1 > > > > sleep 10 > > > > > > # > > # NVT EQUILIBRATION # > > # > > echo "Starting constant volume equilibration..." > > > > cd ../ > > mkdir NVT > > cd NVT > > > > $GMX/gmx grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro > -p > > $FREE_ENERGY/curcumin/topol.top -o nvt$LAMBDA.tpr > > > > $GMX/gmx mdrun -deffnm nvt$LAMBDA -ntmpi 1 > > > > echo "Constant volume equilibration complete." > > > > sleep 10 > > > > # > > # NPT EQUILIBRATION # > > # > > echo "Starting constant pressure equilibration..." > > > > cd ../ > > mkdir NPT > > cd NPT > > > > $GMX/gmx grompp -f $MDP/NPT/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro > -p > > $FREE_ENERGY/curcumin/topol.top -t ../NVT/nvt$LAMBDA.cpt -o > npt$LAMBDA.tpr > > > > $GMX/gmx mdrun -deffnm npt$LAMBDA -ntmpi 1 > > > > echo "Constant pressure equilibration complete." > > > > sleep 10 > > > > > > # > > # PRODUCTION MD # > > # > > echo "Starting production MD simulation..." > > > > cd ../ > > mkdir Production_MD > > cd Production_MD > > > > $GMX/gmx grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c > > ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/curcumin/topol.top -t > > ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr > > > > $GMX/gmx mdrun -deffnm md$LAMBDA -ntmpi 1 > > > > echo "Production MD complete." > > > > # End > > echo "Ending. Job completed for lambda = $LAMBDA" > > > > cd $FREE_ENERGY > > done > > > > exit; > > > > *MDP input file:* > > > > ; Run control > > integrator = steep > > nsteps = 5000 > > ; EM criteria and other stuff > > emtol= 100 > > emstep = 0.01 > > niter= 20 > > nbfgscorr= 10 > > ; Output control > > nstlog = 1 > > nstenergy= 1 > > ; Neighborsearching and short-range nonbonded interactions > > cutoff-scheme= verlet > > nstlist = 1 > > ns_type = grid > > pbc = xyz > > rlist= 1.2 > > ; Electrostatics > > coulombtype = PME > > rcoulomb = 1.2 > > ; van der Waals > > vdwtype = cutoff > > vdw-modifier = potential-switch > > rvdw-switch = 1.0 > > rvdw = 1.2 > > ; Apply long range dispersion corrections for Energy and Pressure > > DispCorr = EnerPres > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; EWALD/PME/PPPM parameters > > pme_order= 6 > > ewald_rtol = 1e-06 > > epsilon_surface = 0 > > ; Temperature and pressure coupling are off during EM > > tcoupl = no > > pcoupl = no > > ; Free energy control stuff > > free_energy = yes > > init_lambda_state= 21 > > delta_lambda = 0 > > calc_lambda_neighbors= 1; only immediate neighboring windows > > couple-moltype = CUR ; name of moleculetype to decouple > > couple-lambda0 = vdw ; only van der Waals interactions > > couple-lambda1
Re: [gmx-users] Simulated Annealing
Use the final configuration to start a new annealing calculation. As there is no real ensemble to preserve, there is nothing to manage. Mark On Sat., 9 Feb. 2019, 10:48 Shan Jayasinghe, wrote: > Dear Gromacs Users, > > How do we extend a simulated annealing? > > Thank you. > > Best Regards > Shan Jayasinghe > -- > 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 (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC conditions for Vacuum simulation
Hi, No. Models without cutoffs will scale badly with particle count. Adding cutoffs is not always a performance win either, because while that saves computation of interactions, it adds the need to periodically search for which particle interactions to compute. Mark On Sat., 9 Feb. 2019, 17:24 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I am trying to model a peptide in gas phase which requires proper > conditions like: no PBC, no cut-offs for VanderWaals and electrostatics, > coulomb type not PME. However, this increases computational time by N^2 for > N number of atoms. Is there a way to mitigate this? > > Many thanks, > Neena > > -- > 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 (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
