[gmx-users] Invallid order of atomtypes

os.itp, line 7 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype I have checked http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx but the top file is fine, accordingly Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://w

[gmx-users] CHARMM2GMX

detected in pfos.str : 3.0.1 WARNING: CGenFF versions are not equivalent! ERROR: Could not detect CGenFF version. Exiting. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes

Re: [gmx-users] ERROR in cgenff_charmm2gmx.py

Cheers Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no

[gmx-users] CR atom name CHARMM27 ff

Hi , I have tried to convert the mol2 to ITP by protparam.org, and apparently it works, nevertheless it gives a CR atom for alkane carbons. This CR is not in the charm27 ff atomtypes. What is the correct name for this? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg

[gmx-users] ERROR in cgenff_charmm2gmx.py

No module named networkx Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.n

Re: [gmx-users] Topolgen and topolbuild

Thanks which of the CHARMM FFs from GMX library is correct for a fluorinated molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47

[gmx-users] Generate GROMACS topology

PS: For those silent wonderers on this topic, SWISSPARAM can do the trick: https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=24554 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun

Re: [gmx-users] Topolgen and topolbuild

PS: generate ITP from STR without CHARMM GUI Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab

Re: [gmx-users] Topolgen and topolbuild

Hi Stephane. Thanks for that. I have tried it, however it generates a str file, and from there how to generate the GMX ITP is unknown. Is there a tutorial that shows how to generate ITP from STR? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no

[gmx-users] Topolgen and topolbuild

Hi, I found these tow programs on GMX site, however they don't work. How can I generate a CHARMM topology to be used in GMX for a charged molecule? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no

[gmx-users] Tutorial

Hi, is there a tutorial for importing fully charged non-peptid topologies for the AMBER FF ISBN type to GMX somewhere ? Thanks Sergio Manzetti Fjordforsk AS Midtun 6894 VangsnesNorge Org.nr. 911 659 654 Tlf: +47 57695621Økolab | Nanofactory

Re: [gmx-users] Charges and Antechamber

Thanks, in which file do you add your residue, do you have an example? Thanks! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621

Re: [gmx-users] Charges and Antechamber

this part? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no

[gmx-users] Charges and Antechamber

Hi, I was wondering what the best approach is to simulate a negatively charged topology imported from ANTECHAMBER (which can't do integral charges): 1. Do QM calculations on the molecule, then edit the output from Antechamber or 2. Do something else. Sergio Manzetti [ http

Re: [gmx-users] *** Spam ? ***Re: Changing position restraints force in GMX

Sounds complex! Thanks Justin Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http

[gmx-users] Changing position restraints force in GMX

Hi, has anyone experience with changing position restrains for DNA in GMX? In case, is it only to change the figure "1" to "0.75" for instance in the itp file? Thanks Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fj

Re: [gmx-users] trjconv not able to generated output

Sorry, my mistake. You better put me away with Zuckerberg and those guys. Have a good weekend! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf

Re: [gmx-users] trjconv not able to generated output

I have done this many times before, its doesn't give any problems, it gives the last frame and only that. But not in this case Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes

[gmx-users] trjconv not able to generated output

, but they don't "appear" after the selection of groups. How can I repair or check a trajectory? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654

Re: [gmx-users] DPOSRES not working

onfout.gro that came out afterwards from using gmx trjconv maybe something irrelated and related to linux command line/rights etc? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Nor

Re: [gmx-users] DPOSRES not working

and XTC came Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no

Re: [gmx-users] DPOSRES not working

://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 2:28:23 PM Subject: Re: [gmx-users] DPOSRES not working On 9/7/17 5:28 AM, Sergio Man

Re: [gmx-users] DPOSRES not working

Hi Johannes, yes, they are there in both cases: ; Include Position restraint file #ifdef POSRES #include "posre_DNA_chain_E.itp" #endif Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |

Re: [gmx-users] DPOSRES not working

AL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water [ molecules ] ; Compound #mols DNA_chain_E 1 DNA_chain_F 1 NA 71 CL 31 PRB 1 SOL 16349 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]

[gmx-users] DPOSRES not working

= 310 gen-seed = 17527 constraints = all-bonds and still, the DNA splits into two Any ideas what could be wrong? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes

Re: [gmx-users] possible bug in posre

://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, August 30, 2017 4:50:55 PM Subject: Re: [gmx-users] possible bug in posre On 8/30/17 10:39 AM, Se

Re: [gmx-users] possible bug in posre

Its only the constraints in DPOSRE that I am concerned about. They do keep the antisense and the sense strands together, however, do they keep this together so that also intercalation between the bases is not any longer physically related? Sergio Manzetti [ http://www.fjordforsk.no

Re: [gmx-users] possible bug in posre

in the box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then any intercalation study is really futile! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894

[gmx-users] possible bug in posre

-bonds Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory

[gmx-users] gmx distance

;DNA" (1333 atoms) Specify any number of selections for option 'select' (Position pairs to calculate distances for): (one per line, for status/groups, 'help' for help, Ctrl-D to end) > 1 Selection '1' parsed > 4 Selection '4' parsed > however, then, which command to issue t

[gmx-users] Missing values in enery EDR

Hi, when running gmx energy on a simulation ouput, I get: --- 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential 13 Pres.-DC

Re: [gmx-users] DNA splitting in simulations

://www.gromacs.org/Documentation/Errors Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab

Re: [gmx-users] DNA splitting in simulations

Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in the email, grompp wanted equal number of tcouplings as groups in the top file. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no

[gmx-users] DNA splitting in simulations

-grps = SOL DNA NA CL tau-t = 0.1 0.1 0.1 0.1 Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it wouldn't proceed. Thanks! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no

[gmx-users] Scaling GROMACS

help in subdividing the tasks? Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab

Re: [gmx-users] Gigantic boxes

Thanks, that fixed it! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http

[gmx-users] Box size and Force field

the problem of rlist being too high and the box size too small. Increasing box size or decreasing rlist does not help. Nothing can be made unless changing force field, because all other options have been tried. Does anyone know an option that can solve this ? Sergio Sergio Manzetti

[gmx-users] Gigantic boxes

in the large water molecule number? Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http

Re: [gmx-users] Domain decomposition

Thanks! I reduced the number to 4, and it works: gmx mdrun -v -dds 0.37 -nt 4 Cheers Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47

Re: [gmx-users] Domain decomposition

Checked the link, nothing written here on rcon and dds... Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com

Re: [gmx-users] MDP for DNA with ions

equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun

[gmx-users] Domain decomposition

--- Not sure what to do here.. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http

Re: [gmx-users] MDP for DNA with ions

OK, thanks for this! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http

Re: [gmx-users] MDP for DNA with ions

tau-t = 0.1 0.1 0.1 0.1 ref-t = 310 310 310 310 Pcoupl = No tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 gen-vel = yes gen-temp = 310 gen-seed = 173529 constraints = all-bonds Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no

Re: [gmx-users] Genion

Indeed. Thanks! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no

Re: [gmx-users] Genion

THanks Justin. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no

Re: [gmx-users] Genion

for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors How can I fix the system, when the energy minimization step cannot? Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http

Re: [gmx-users] Genion

does not match (NA - Na) Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no

Re: [gmx-users] Genion

names from topol.top will be used atom names from dna_solv_NaCl.gro will be ignored Giving the mdrun problem.. Not sure how to get by this! Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no

Re: [gmx-users] Genion

Indeed, thanks: I did it manually. Will try updating the top with genion, Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47

Re: [gmx-users] Genion

topol_solvated -o dna_solv_NaCl_EM gmx mdrun This worked. Then for the sim: dna_solv_NaCl_EM.gro does not contain any ions. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge

[gmx-users] Genion

, and the procedure is therefore not working. Why is this so? Does one have to do the genion procedure each time one wants to use gromp with a new mdp file? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894

Re: [gmx-users] Error running GMX 5.14

Thanks, this worked. Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http

Re: [gmx-users] Protein-ligand binding Cut-offs

Yes, remove figure reference, use figures from us, and insert reference at the same place for the Software: "Figure made with MacMolPlt" http://www.sciencedirect.com/science/article/pii/S109332639929 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg

Re: [gmx-users] Error running GMX 5.14

Precisely. Thanks. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http

Re: [gmx-users] Error running GMX 5.14

One simple question, where does one get the sytem input for genion, as it only want tpr, unless one uses grompp? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr

Re: [gmx-users] Error running GMX 5.14

://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Tuesday, June 20, 2017 4:21:18 PM Subject: Re: [gmx-users] Error running GMX 5.14 On 6/20/17 10:14 AM, Sergio Manzetti

Re: [gmx-users] Error running GMX 5.14

OK Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory

Re: [gmx-users] Error running GMX 5.14

Thanks Justin. So it is right to run the simulation without ions, then add ions, then re-run with ions with the new topolgy? Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894

Re: [gmx-users] Error running GMX 5.14

? Thanks Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no

Re: [gmx-users] Error running GMX 5.14

I can add ions to the final system, after having simulated it without ions. But what would the point be? This is the strange thing, genion treats only tpr files, and not gro files with solvated states Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no

Re: [gmx-users] Error running GMX 5.14

__ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sergio Manzetti <sergio.manze...@fjordforsk.no> Sent: Tuesday, June 20, 2017 7:48 AM To: gmx-us...@gromacs.org Subject: [gmx-users] Error run

Re: [gmx-users] Error running GMX 5.14

__ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sergio Manzetti <sergio.manze...@fjordforsk.no> Sent: Tuesday, June 20, 2017 7:48 AM To: gmx-us...@gromacs.org Subject: [gmx-users] Error run

[gmx-users] Error running mdrun em with Sodium ions in GMX 5.14

added to the system by replacing 20 water molecules, which grompp thinks are waters. The index file does not contain info about these, as also there, the Sodium are not identified and differentiated from water molecules. What is the best approach here to correct this? Thanks! Sergio Manzetti

[gmx-users] Error running GMX 5.14

! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory

[gmx-users] CNT simulation

Dear all, given the tedious process of building topologies of short finite nanotube systems for GROMACS 4.6.5, gaff force field, it would be nice to know if someone could do the task for a moderate fee. all the best sergio