Re: [gmx-users] REMD mdrun_mpi error
Hi Mark,
I tried to run an individual tpr file and it crashed:
Double sids (0, 1) for atom 26
Double sids (0, 1) for atom 27
Double sids (0, 1) for atom 28
Double sids (0, 1) for atom 29
Double sids (0, 1) for atom 30
Double sids (0, 1) for atom 31
Double sids (0, 1) for atom 32
Double sids (0, 1) for atom 33
Double sids (0, 1) for atom 34
Double sids (0, 1) for atom 35
Double sids (0, 1) for atom 36
Double sids (0, 1) for atom 37
Double sids (0, 1) for atom 38
Double sids (0, 1) for atom 39
Double sids (0, 1) for atom 40
---
Program mdrun, VERSION 4.6.5
Source code file:
/local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c,
line: 99
Fatal error:
Double entries in block structure. Item 53 is in blocks 1 and 0
Cannot make an unambiguous inverse block.
To create my tpr files I useda bash script like this:
*#!/bin/bash -fnrep=`wc temperatures.dat | awk '{print $1}'`echo
$nrepcount=0count2=-1for TEMP in `cat temperatures.dat`do let count2+=1
REP=`printf %03d $count2` REPBIS=`printf %d $count2` echo
TEMPERATURE: $TEMP K == FILE: nvt_$REP.mdp sed s/X/$TEMP/g
nvt.mdp nvt_$REP.mdp grompp -f nvt_$REP.mdp -c min.gro -p topol.top -o
eq_$REPBIS.tpr -maxwarn 1 rm -f tempdoneecho N REPLICAS = $nrepecho
Done.*
Nawel
2015-06-23 11:47 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com:
Hi,
Do your individual replica .tpr files run correctly on their own?
Mark
On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele nawel.m...@gmail.com wrote:
Dear gromacs users,
I am trying to simulate a ligand using REMD method in explicit solvent
with
the charmm force field. When I try to equilibrate my system I get this
error :
Double sids (0, 1) for atom 26
Double sids (0, 1) for atom 27
Double sids (0, 1) for atom 28
Double sids (0, 1) for atom 29
Double sids (0, 1) for atom 30
Double sids (0, 1) for atom 31
Double sids (0, 1) for atom 32
Double sids (0, 1) for atom 33
Double sids (0, 1) for atom 34
Double sids (0, 1) for atom 35
Double sids (0, 1) for atom 36
Double sids (0, 1) for atom 37
Double sids (0, 1) for atom 38
Double sids (0, 1) for atom 39
Double sids (0, 1) for atom 40
---
Program mdrun_mpi, VERSION 4.6.5
Source code file:
/local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c,
line: 99
Fatal error:
Double entries in block structure. Item 53 is in blocks 1 and 0
Cannot make an unambiguous inverse block.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
*My mdp input file looks like this :*
*title = CHARMM compound NVT equilibration define =
-DPOSRES ; position restrain the protein; Run
parametersintegrator = sd; leap-frog stochastic dynamics
integratornsteps = 100 ; 2 * 100 = 100
psdt = 0.002 ; 2 fs; Output controlnstxout =
500 ; save coordinates every 0.2 psnstvout =
10; save velocities every 0.2 psnstenergy = 500
; save energies every 0.2 psnstlog = 500 ; update log
file every 0.2 ps; Bond parameterscontinuation= no; first
dynamics runconstraint_algorithm = SHAKE; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds)
constrainedshake-tol = 0.1 ; relative tolerance for
SHAKE;
Neighborsearchingns_type = grid ; search neighboring
grid
cellsnstlist = 5 ; 10 fsrlist = 1.0
; short-range neighborlist cutoff (in nm)rcoulomb= 1.0
;
short-range electrostatic cutoff (in nm)rvdw= 1.0 ;
short-range van der Waals cutoff (in nm); Electrostaticscoulombtype =
PME ; Particle Mesh Ewald for long-range
electrostaticspme_order = 4 ; Interpolation order for
PME. 4 equals cubic interpolationfourierspacing = 0.16 ; grid
spacing for FFT; Temperature coupling is on;tcoupl = V-rescale
; modified Berendsen thermostattc-grps = LIG SOL ; two
coupling groups - more accuratetau_t = 1.0 1.0 ; time
constant, in psref_t = X X ; reference
temperature, one for each group, in K;Langevin dynamicsbd-fric =
0
; ;Brownian dynamics friction coefficient. ld-seed
=-1;;pseudo random seed is used; Pressure coupling is
offpcoupl = no; no pressure coupling in NVT;
Periodic
boundary conditionspbc = xyz ; 3-D PBC; Dispersion
correctionDispCorr= EnerPres ; account for cut-off vdW
scheme;
Velocity
[gmx-users] constraint pull code / gromacs 5.0.4
Dear gromacs users, I'm using the pull code to evaluate the Potential of Mean Forces between two nanoparticles(NPs) of Radius = 1nm. Specifically, in order to create the configurations (i.e.the 2 NPs at different centr of mass distance) I used the constraint pull code. Then for each configuration I run a simulation of 2ns. Part of the mdp file that I used is: ... ; 9) NEIGHBOR SEARCHING ; cut-off scheme cutoff-scheme = Verlet nstlist = 10; ns_type = grid pbc= xyz periodic_molecules = yes rlist = 1.3 ; ; 10) ELECTROSTATICS coulombtype = PME-Switch ; pme_order = 4 rcoulomb= 1.3 ; rcoulomb-switch = 1.25 ; ; 11) VdW vdw-type= Cut-off ; rvdw-switch = 1.3 ; rvdw= 1.3 DispCorr= EnerPres ; ; 13) EWALD fourierspacing = 0.12 ; (0.12) [nm] default fourier_nx = 0 ; (0) default fourier_ny = 0 ; (0) default fourier_nz = 0 ; (0) default ewald_rtol = 1e-5 ; (1e-5) default optimize_fft= yes ; 14) TEMPERATURE COUPLING Tcoupl = Nose-Hoover tc_grps = UNKSOL tau_t = 0.10.1 ref_t = 300300 ; 15) PRESSURE COUPLING Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 2 2; (1) [ps] default compressibility = 4.5e-5 4.5e-5 ; [bar-1] ref_p = 11; [bar] refcoord_scaling= com; ; 17) VELOCITY GENERATION gen-vel = no gen-temp = 300 gen-seed = -1 ; 18) BONDS constraints = ; convert all bonds to constraints constraint_algorithm= ; LINear Constraint Solver continuation= yes ; lincs_order = 4 ; lincs_iter = 1 ; lincs_warnangle = 90; ; Pull type: pull = constraint; pull-geometry= distance ; pull-dim = Y N N ; pull-start = yes ; pull-ngroups = 2 ; pull-group1-name = 1UNK ; pull-group2-name = 2UNK pull-coord1-groups = 1 2 pull-coord1-rate = 0.0 ; 0.01 nm per ps pull-nstxout = 1000 ; every 2 ps pull-nstfout = 1000 ; every 2 ps pull-coord1-init = 0.0 ; My problem is related to the resulting forces that I obtained. They do not seem to converge and they are really fluactuating for any configuration (i.e. indipendently from the com distance) An example of pullf.xvg that I obtained at 2 nm com distance .. 1992.5000 -2367.46 1993. -6738.59 1993.5000 361.472 1994. 647.644 1994.5000 -6222.61 1995. 6018.37 1995.5000 1921.95 1996. -1618.72 1996.5000 1279.2 1997. 1302.08 1997.5000 2256.82 1998. 1485.05 1998.5000 2318.51 1999. -3588.26 1999.5000 979.835 2000. -678.607 Of course, the PMF that I got with a simple intagration of the forces is characterized by enormous error bars and its shape does not have any sense. Do you have some suggestions for getting converged forces? Do you see some errors in the mdp file? Thank you in advance for your help. Annalisa Annalisa Cardellini, M.Sc. Ph.D. student Politecnico di Torino - Energy Department Corso Duca degli Abruzzi, 24 10129 Turin - ITALY Tel: +39-011-090-4495 Fax: +39-011-090-4499 E-mail: annalisa.cardell...@polito.it SMaLL: http://www.polito.it/small -- 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] installation errors
Thanks Mark! I could install it at last. I installed it in a desired directory not in root, used --enable-shared and --disable-float. that was the only way it was installed! and I should say I tried from all versions 5 to 4 and finally the one without errors was 4.5.5! (with fftw-3.3.4) I have 2 questions now: is it ok not to have gromacs installed in root? when I want to run is it necessary to have the file in the directory installed? and does double precision work the same as single?(I can see _d after commands) thanks alot On Mon, Jun 22, 2015 at 11:14 PM, mah maz mahma...@gmail.com wrote: Thanks Parvez! but it was not the solution. do you have any other ideas to help? On Sun, Jun 21, 2015 at 1:42 PM, mah maz mahma...@gmail.com wrote: Dear all, I am trying to install a new version of gromacs(rather than rpm) on my system. I apply these commands:(in root while im superuser) tar -xzvf fftw-3.3.4.tar.gz cd fftw-3.3.4 ./configure --enable-float --enable-threads make make install and for gromacs: tar -xzvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure make after this command the following errors occur: can not be used when making a shared object recompile with -fPIC /usr/local/lib64/libfftw3.a:couldnt read symbols:bad value collect2: error: ld returned 1 exit status make[3]:***[libmd.la] error1 make[3]: leaving directory '/gromacs-4.5.5/src/mdlib make[2]: [all-recursive] error1 make[2]: leaving directory '/gromacs-4.5.5/src make[1]: error2 make[1]: leaving directory '/gromacs-4.5.5/src make***[all-recursive] error1 what should i do? is it because of the incompatibility of the fftw version and gromacs version? thanks! -- 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] Does Gromacs take advantage of ECC memory?
Dear Andrew, ECC is Error Correction Code for the memory and is not related to you application. For a single-user workstation, you generally don't need the ECC. It is more important in servers. Not every motherboard supports ECC and most desktop motherboards do not, so if you do get it, you should be sure that your motherboard (not your app) can utilize ECC memory. Peter Stern Weizmann Institute of Science -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Andrew DeYoung Sent: Tuesday, June 23, 2015 6:36 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Does Gromacs take advantage of ECC memory? Hi, I'm looking into a workstation which I will use to run some Gromacs simulations. I'm a chemist, not a computer person, so I'm not very well-versed in computer hardware. I have the option of getting non-ECC or ECC memory, with the ECC being at extra cost. In asking around about whether I need ECC, I've been advised to research your simulation apps and see if they can take advantage of ECC. I don't see ECC mentioned in the manual. Does Gromacs take advantage of ECC? The simulations I will be running will not be terribly large: on the order of ~10,000 atoms for a few tens of ns. My system will likely have 8 cores. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- 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] Protein-DNA simulation LINKS error
On 6/23/15 7:13 AM, Timofey Tyugashev wrote: I'm trying a few simulations of a enzyme-DNA complex and while in short timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation crashes with numerous LINCS warnings. Maybe there are some errors in mdp configuration file? To mine inexperienced eye they look good enough. I'm using AMBER99SB-ILDN with TIP3 water model and 1.0 dodecahedron water box, system requires around 30 Na atoms to compensate the charge. I also create a combined group Protein_DNA using make ndx. Here are the MDPs: Ions: http://pastebin.com/xCUqiDM0 EM: http://pastebin.com/WcXdXBWf NVT: http://pastebin.com/sdVqfGDM NPT: http://pastebin.com/AsMVC7yH MD: http://pastebin.com/sne7Fpzt Any help? AMBER99sb-ILDN uses different cutoffs so correct those, but that alone is not necessarily to blame for the crash. In general, here's the usual troubleshooting protocol: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Does Gromacs take advantage of ECC memory?
On 23/06/15 20:33, Peter Stern wrote: Dear Andrew, ECC is Error Correction Code for the memory and is not related to you application. For a single-user workstation, you generally don't need the ECC. It is more important in servers. Not every motherboard supports ECC and most desktop motherboards do not, so if you do get it, you should be sure that your motherboard (not your app) can utilize ECC memory. GROMACS does check memory errors on GPUs, in particular cheap GPUs sometimes have cheap memory, while the more expensive GPUs have ECC memory. Peter Stern Weizmann Institute of Science -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Andrew DeYoung Sent: Tuesday, June 23, 2015 6:36 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Does Gromacs take advantage of ECC memory? Hi, I'm looking into a workstation which I will use to run some Gromacs simulations. I'm a chemist, not a computer person, so I'm not very well-versed in computer hardware. I have the option of getting non-ECC or ECC memory, with the ECC being at extra cost. In asking around about whether I need ECC, I've been advised to research your simulation apps and see if they can take advantage of ECC. I don't see ECC mentioned in the manual. Does Gromacs take advantage of ECC? The simulations I will be running will not be terribly large: on the order of ~10,000 atoms for a few tens of ns. My system will likely have 8 cores. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- 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. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] constraint pull code / gromacs 5.0.4
On 6/23/15 4:28 PM, Alex wrote: It's dangerous to make broad generalizations like constraints should be deprecated. Sometimes constraints are not appropriate (materials, crystals, etc). But for the vast majority of biomolecular simulations, we really don't care about different vibrational states of bonds involving H, so there's zero purpose to running our simulations 4x slower just to collect information we don't need :) Here he is. :) My not entirely serious comment aside (and not to hijack the thread), how is the analytical calculation of forces in harmonic springs computationally heavier than something like SHAKE or LINCS? Are you guys doing something algorithmically superfancy with LINCS? I recall implementing both SHAKE and LINCS and for the life of me can't see where the x4 factor comes from. It has nothing to do with the computational cost of bonds vs. constraints; it's the time step. Without constraints, dt = 0.5 fs (maybe 1.0 fs if you're lucky) and with constraints (I don't care which algorithm, but LINCS is generally more stable), dt = 2.0 fs. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] gas phase force field
On 6/23/15 12:45 AM, Swapnil Kate wrote: hello, Thanks for yours valuable comments, So Which force fields do you people recommend to simulate gas phase systems?Can we simulate gas and liquid mixtures in one go? What does your evaluation of the literature tell you? Which force fields do people use, and how accurate are the data they have obtained? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] constraint pull code / gromacs 5.0.4
On 6/23/15 2:10 PM, Alex wrote: The pulling rate, as it appears in your mdp, is actually zero. That aside, ...which is correct if one is sampling independent windows and collecting the forces to reconstruct the PMF. What is atypical is the application of a constraint rather than a harmonic potential. The typical umbrella in umbrella sampling. we do not have enough info about the system. What are the nanoparticles made of? What forcefield is being used? Can you use trjconv to see what's going on? Please check that your system is happy prior to pulling. The huge variation in forces could mean weird pulling behavior (which does happen), or that your particles are breathing. Set constraints to 'none' and pull code to see if your system behaves. The use of constraints should be deprecated in general, but I fear for my life suggesting it here. It's dangerous to make broad generalizations like constraints should be deprecated. Sometimes constraints are not appropriate (materials, crystals, etc). But for the vast majority of biomolecular simulations, we really don't care about different vibrational states of bonds involving H, so there's zero purpose to running our simulations 4x slower just to collect information we don't need :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] gas phase force field
OPLS is a good choice to start with On Tue, Jun 23, 2015 at 1:45 AM, Swapnil Kate swapnilk...@rocketmail.com wrote: hello, Thanks for yours valuable comments, So Which force fields do you people recommend to simulate gas phase systems? Can we simulate gas and liquid mixtures in one go? Regards Swapnil On Monday, 22 June 2015 6:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/22/15 8:47 AM, V.V.Chaban wrote: Not all organics is polar, Justin. :-) Obviously. Hydrogen bond length, and hence, energy are well limited by sigma in LJ. Even if dipole moments are overestimated by 20%, this should not lead to a proportional increase in the hydrogen bond strength. Actually, it can and does. I used a specific example that we know quite well. Overestimation of dipole moments in vicinal alcohols depresses the gas-phase energy leading to incorrect dHvap. This is a trend in additive force fields, and we consistently see failures of additive models to respond to different conditions as we develop our polarizable force fields (which correctly reproduce both gas and liquid phase properties). Most force fields are geared towards condensed phase properties. Of course not all models reflect the same properties, but one needs to carefully evaluate the proper behavior in the gas phase based on available data. Additive models are generally incapable of responding to both gas and liquid states. -Justin On Sun, Jun 21, 2015 at 9:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/21/15 9:07 AM, V.V.Chaban wrote: Actually, any existing field, since all of them -- to this or that extent -- were cteated under cluster-in-vacuum' approach. While most biomolecular force fields have their origins in gas-phase QM, most ultimately target condensed-phase properties. Additive force fields thus must overestimate gas-phase dipole moments on the order of ~20% or more to capture proper liquid-phase properties. This is a reason why one will see overly strong intramolecular hydrogen bonding in polyols, etc. -Justin On Sun, Jun 21, 2015 at 3:02 AM, Swapnil Kate swapnilk...@rocketmail.com wrote: Hello all, Can any one please tell me which force fields are used for accurate prediction of gas phases on organics? RegardsSwapnil -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Protein-DNA simulation LINKS error
I have ordinary DNA and an oxoguanine site? What actions should I take to correct these vsite parameters? Message: 1 Date: Tue, 23 Jun 2015 22:24:20 + From: Erik Marklund erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA simulation LINKS error Message-ID: 61edbf38-6d1f-4089-8ebe-03caaaff6...@chem.ox.ac.uk Content-Type: text/plain; charset=us-ascii The vsite parameters are not complete for DNA/RNA. Perhaps you have faster oscillations in your system than you intended to have. Erik On 23 Jun 2015, at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 6/23/15 7:13 AM, Timofey Tyugashev wrote: I'm trying a few simulations of a enzyme-DNA complex and while in short timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation crashes with numerous LINCS warnings. Maybe there are some errors in mdp configuration file? To mine inexperienced eye they look good enough. I'm using AMBER99SB-ILDN with TIP3 water model and 1.0 dodecahedron water box, system requires around 30 Na atoms to compensate the charge. I also create a combined group Protein_DNA using make ndx. Here are the MDPs: Ions: http://pastebin.com/xCUqiDM0 EM: http://pastebin.com/WcXdXBWf NVT: http://pastebin.com/sdVqfGDM NPT: http://pastebin.com/AsMVC7yH MD: http://pastebin.com/sne7Fpzt Any help? AMBER99sb-ILDN uses different cutoffs so correct those, but that alone is not necessarily to blame for the crash. In general, here's the usual troubleshooting protocol: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] About g_helix
Hello, Is it possible to calculate the average twist, turn, rise etc of a DNA molecule using g_helix? I am trying to show how the native conformation of the nucleic acid gets distorted on interacting with some carbon based nanoparticles. if yes, can anyone help me understanding how it works? Many thanks in advance. Soumadwip Ghosh Research Fellow IITB India -- 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] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5
Hi, On Tue, Jun 23, 2015 at 10:07 AM Makoto Yoneya makoto-yon...@aist.go.jp wrote: Dear GROMACS users: I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5 (e.g. cmake -DGMX_LARGEFILES=OFF bra-bra). At the end of cmake, it says CMake Warning: Manually-specified variables were not used by the project: GMX_LARGEFILES. Although, there are lines, include(gmxTestLargeFiles) gmx_test_large_files(GMX_LARGEFILES) in CMakeLists.txt file, this test looks skipped in actual cmake (no message on this test). Any info.s on this subject will be welcome! Setting that variable skips running the tests for the availability of various size-dependent file operations (and since such a skip seems useless, we should probably remove the variable entirely). I suggest you remove your build tree and try again without setting it. Why did you decide to try to set it? Mark Regards, Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- 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] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5
Dear GROMACS users: I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5 (e.g. cmake -DGMX_LARGEFILES=OFF bra-bra). At the end of cmake, it says CMake Warning: Manually-specified variables were not used by the project: GMX_LARGEFILES. Although, there are lines, include(gmxTestLargeFiles) gmx_test_large_files(GMX_LARGEFILES) in CMakeLists.txt file, this test looks skipped in actual cmake (no message on this test). Any info.s on this subject will be welcome! Regards, Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- 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] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5
Hi, yes the variable is ignored. Because with GROMACS 5 large file support is required. Thus if the variable is set to false it also prints a fatal error. It was never a variable which was suppose to be set by the user. Why do you ask? What do you try to achieve? Roland On Tue, Jun 23, 2015 at 3:50 AM, Makoto Yoneya makoto-yon...@aist.go.jp wrote: Dear GROMACS users: I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5 (e.g. cmake -DGMX_LARGEFILES=OFF bra-bra). At the end of cmake, it says CMake Warning: Manually-specified variables were not used by the project: GMX_LARGEFILES. Although, there are lines, include(gmxTestLargeFiles) gmx_test_large_files(GMX_LARGEFILES) in CMakeLists.txt file, this test looks skipped in actual cmake (no message on this test). Any info.s on this subject will be welcome! Regards, Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] calculation of total no of hydrogen bond present in the system
Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs topology and coordinate through acpype.py. Now how to specify no of donor and acceptor for water molecules. Total 350 water molecules is there in my system . So there should be two H bond donor and two H bond acceptor, but during calculation it is showing 350 donor and 350 acceptor. Thanks Rahman -- 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] (no subject)
Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs topology and coordinate through acpype.py. Now how to specify no of donor and acceptor for water molecules. Total 350 water molecules is there in my system . So there should be two H bond donor and two H bond acceptor, but during calculation it is showing 350 donor and 350 acceptor. Thanks -- 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] calculation of total no of hydrogen bond present in the system
Dear Rahman, The donors are not the hydrogens, but the oxygens to which they are bonded. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 23 Jun 2015, at 11:08, MOHD HOMAIDUR RAHMAN rahman...@gmail.com wrote: Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs topology and coordinate through acpype.py. Now how to specify no of donor and acceptor for water molecules. Total 350 water molecules is there in my system . So there should be two H bond donor and two H bond acceptor, but during calculation it is showing 350 donor and 350 acceptor. Thanks Rahman -- 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] About g_helix
Hello, Is it possible to calculate the average twist, turn, rise etc of a DNA molecule using g_helix? I am trying to show how the native conformation of the nucleic acid gets distorted on interacting with some carbon based nanoparticles. if yes, can anyone help me understanding how it works? Many thanks in advance. Soumadwip Ghosh Research Fellow IITB India -- 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] REMD mdrun_mpi error
Hi, Do your individual replica .tpr files run correctly on their own? Mark On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele nawel.m...@gmail.com wrote: Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to equilibrate my system I get this error : Double sids (0, 1) for atom 26 Double sids (0, 1) for atom 27 Double sids (0, 1) for atom 28 Double sids (0, 1) for atom 29 Double sids (0, 1) for atom 30 Double sids (0, 1) for atom 31 Double sids (0, 1) for atom 32 Double sids (0, 1) for atom 33 Double sids (0, 1) for atom 34 Double sids (0, 1) for atom 35 Double sids (0, 1) for atom 36 Double sids (0, 1) for atom 37 Double sids (0, 1) for atom 38 Double sids (0, 1) for atom 39 Double sids (0, 1) for atom 40 --- Program mdrun_mpi, VERSION 4.6.5 Source code file: /local/software/gromacs/4.6.5/source/gromacs-4.6.5/src/gmxlib/invblock.c, line: 99 Fatal error: Double entries in block structure. Item 53 is in blocks 1 and 0 Cannot make an unambiguous inverse block. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors *My mdp input file looks like this :* *title = CHARMM compound NVT equilibration define = -DPOSRES ; position restrain the protein; Run parametersintegrator = sd; leap-frog stochastic dynamics integratornsteps = 100 ; 2 * 100 = 100 psdt = 0.002 ; 2 fs; Output controlnstxout = 500 ; save coordinates every 0.2 psnstvout = 10; save velocities every 0.2 psnstenergy = 500 ; save energies every 0.2 psnstlog = 500 ; update log file every 0.2 ps; Bond parameterscontinuation= no; first dynamics runconstraint_algorithm = SHAKE; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrainedshake-tol = 0.1 ; relative tolerance for SHAKE; Neighborsearchingns_type = grid ; search neighboring grid cellsnstlist = 5 ; 10 fsrlist = 1.0 ; short-range neighborlist cutoff (in nm)rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm)rvdw= 1.0 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order = 4 ; Interpolation order for PME. 4 equals cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is on;tcoupl = V-rescale ; modified Berendsen thermostattc-grps = LIG SOL ; two coupling groups - more accuratetau_t = 1.0 1.0 ; time constant, in psref_t = X X ; reference temperature, one for each group, in K;Langevin dynamicsbd-fric = 0 ; ;Brownian dynamics friction coefficient. ld-seed =-1;;pseudo random seed is used; Pressure coupling is offpcoupl = no; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr= EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp= 0.0 ; temperature for Maxwell distributiongen_seed= -1; generate a random seed* *And my input file to run it in parallel looks like that:* *#!/bin/bash#PBS -l nodes=3:ppn=16#PBS -l walltime=00:10:00#PBS -o zzz.qsub.out#PBS -e zzz.qsub.errmodule load openmpi module load gromacs/4.6.5mpirun -np 48 mdrun_mpi -s eq_.tpr -multi 48 -replex 10 faillog-X.log* Does anyone have seen this issue before?? Many thanks, -- Nawel Mele, PhD Research Student Jonathan Essex Group, School of Chemistry University of Southampton, Highfield Southampton, SO17 1BJ -- 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] Umbrella Sampling problem
Dear all, I follow the Umbrella Sampling tutorial, and have some problems:1. pdb2gmx with -ter have warning TYR-1 missiong H2. grompp -f npt_umbrella.mdp have 1 warning, but I avoid it.3. Gromacs 4.6.7 and gromacs 5.0.4 have same result: energy minimum is 24.8 kcal mol-1So, what happed in my simulations ? The result is wrong or not ? and how can I do?Thanks! -- 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] REMD with different structures
Hi I am trying to do NVT REMD simulations with gromacs. I have 60 replicas and each of them have different starting structure . The starting structures have same number of atoms but slightly different volume and pressure. I was able to run these simulations but I want to know if having different volume and pressure is affecting the exchange probability, and if it does, is it being included in the gromacs REMD simulations ? Please suggest a method to verify it . -- Regards Ruchi Lohia Graduate Student -- 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] Protein-DNA simulation LINKS error
The vsite parameters are not complete for DNA/RNA. Perhaps you have faster oscillations in your system than you intended to have. Erik On 23 Jun 2015, at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 6/23/15 7:13 AM, Timofey Tyugashev wrote: I'm trying a few simulations of a enzyme-DNA complex and while in short timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation crashes with numerous LINCS warnings. Maybe there are some errors in mdp configuration file? To mine inexperienced eye they look good enough. I'm using AMBER99SB-ILDN with TIP3 water model and 1.0 dodecahedron water box, system requires around 30 Na atoms to compensate the charge. I also create a combined group Protein_DNA using make ndx. Here are the MDPs: Ions: http://pastebin.com/xCUqiDM0 EM: http://pastebin.com/WcXdXBWf NVT: http://pastebin.com/sdVqfGDM NPT: http://pastebin.com/AsMVC7yH MD: http://pastebin.com/sne7Fpzt Any help? AMBER99sb-ILDN uses different cutoffs so correct those, but that alone is not necessarily to blame for the crash. In general, here's the usual troubleshooting protocol: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5
Dear Mark and Roland: Thank you for response. Why did you decide to try to set it? Why do you ask? What do you try to achieve? For me, I found it is necessary to compile gromacs with MinGW32 on 32bit windows PC. Up to gromacs-4.6.7, it works without any troubles for me (see https://staff.aist.go.jp/makoto-yoneya/MDonWINPC/ for full cmake options.) The reason to try MinGW (not Cygwin) is it runs standalone in command prompt of windows PC. I'd been using this gromacs compiled MinGW for short practice class for primers. It is much easier than the Cygwin version because we can skip troublesome Cygwin installation and explanation of some linux commands. I'm very happy to hear the way to re-activate GMX_LARGEFILES option or way to compile with MinGW32 without using this. Regards, Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- 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.
