Dear Justin the results of EM was: Steepest Descents converged to Fmax < 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern
On Tue, May 1, 2012 at 9:33 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: POPC: ff53a6 and CHARMM36 formats (Justin A. Lemkul) > 2. Re: segmentation fault during equilibration (Justin A. Lemkul) > 3. Re: minimum distance between periodic images does not aggree > with box dimensions (Tsjerk Wassenaar) > 4. saltbridges newbie question (Denis Kazakiewicz) > 5. Re: disre and posres together? (Mark Abraham) > 6. Re: saltbridges newbie question (Peter C. Lai) > 7. Re: saltbridges newbie question (Denis Kazakiewicz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 01 May 2012 08:16:14 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f9fd40e.5070...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 5/1/12 8:05 AM, Ángel Piñeiro wrote: >> I guess there are better solutions but an alternative is to map your bilayer >> to >> MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE >> (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom >> CHARMM36. >> > > Even simpler would be to fix the offending atom names and build a suitable > .hdb > entry (if one does not already exist) and produce the topology with pdb2gmx. > I > would think it would then be far easier to preserve the original > configurations > of the lipids, rather than changing the resolution back and forth. > > -Justin > >> Hope it helps, >> >> Ángel. >> >> >> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote: >>> Hi ALL, >>> >>> >>> I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS >>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using >>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming >>> conventions >>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives error. >>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC >>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in >>> advance. >>> >>> >>> >>> >>> Regards, >>> >>> >>> Anirban >>> -- >>> gmx-users mailing listgmx-us...@gromacs.org <mailto:gmx-users@gromacs.org> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive >>> athttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it togmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Tue, 01 May 2012 08:42:26 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] segmentation fault during equilibration > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f9fda32.6010...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 5/1/12 7:19 AM, niaz poorgholami wrote: >> Dear gmx users, >> I am simulating a system including carbon nanotube(a finite >> one)+water+surfactant and so far I have done these things: >> 1.I generated the topology of CNT ( opls force field) by this command: >> g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT >> 2.I used TopolGen to produce topology of surfactant and I calculated >> the charges of atomes by the RESP method and checked the >> atomtypes to make sure that they make sence as well.so I changed some >> atomtypes according to the opls. >> 3.I build a topol.top file that contains topolgy of CNT+surfactant. >> 4.I created the initial configuration for the CNT+surfactant by means >> of packmol. >> 5.I used editconf and genbox with these command: >> editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic > > Unrelated to the crash, but if your longest cutoff is 1.4 nm, setting a > solute-box distance of 0.7 nm will lead to trouble if you ever use NPT. With > just a small fluctuation in box dimension, you can easily violate the minimum > image convention. > >> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro >> 6.I run grompp and genion for adding the ions: >> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr >> genion -s ions.tpr -p topol.top -o solv_ions.gro -nname BR -nn 28 >> 7.I run grompp again for energy minimization: >> grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr >> mdrun -deffnm em >> the em_real.mdp file contains: >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 1000.0 ; Stop minimization when the maximum force< >> 10.0 kJ/mol >> emstep = 0.01 ; Energy step size >> nsteps = 70000 ; Maximum number of (minimization) >> steps to perform >> energygrps = UNK LIG ; Which energy group(s) to write to disk >> >> ; Parameters describing how to find the neighbors of each atom and how >> to calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor >> list and long range forces >> ns_type = grid ; Method to determine neighbor list >> (simple, grid) >> rlist = 0.9 ; Cut-off for making neighbor list (short >> range forces) >> coulombtype = PME ; Treatment of long range electrostatic >> interactions >> rcoulomb = 0.9 ; long range electrostatic cut-off >> rvdw = 1.4 ; Periodic Boundary Conditions (yes/no) >> pbc = xyz ; Periodic Boundary Conditions (yes/no) >> > > What was the outcome of EM? What were your values for Fmax and Epot? > >> 8.then I made an index file for CNT and surfactant and used genrestr >> to restraint the CNT and surfactant during equilibration. >> 9.I run grompp and mdrun with these command:grompp -f nvt.mdp -c >> em.gro -p topol.top -o nvt.tpr -n index.ndx >> mdrun -deffnm nvt >> and after passing 42900 of 50000 steps, segmentation fault occured.I >> checked the log file but it did not contain any errors and I also used >> VMD to see trajetory but I did not see anything wrong. >> I would be pleased if anyone could help me how to fix this. > > We need to see your complete .mdp file for the NVT run. As of now, there is > no > indication of what is wrong. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Tue, 1 May 2012 14:59:56 +0200 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] minimum distance between periodic images does > not aggree with box dimensions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cabze1sjrk2cm_z1y1ddqwvspwdukjeu3ox636a-fkrq2b7y...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Thomas, > > The rhombic dodecahedron is built as a rectangular brick, which makes > it easy to fill with a rectangular bricklet of water. Now, for the > smaller distances the short edge of the rectangular brick is smaller > than the diameter of the particle, and it is represented fragmented. > Best way to get acquainted with this stuff is drawing a circle, and a > hexagon around it. Then tesselate a patch of space and draw the > corresponding rectangular cell. Try to translate the rectangle such > that the whole circle fits in. Good luck! :p > > For the other thing, notice that the distance reported is close to a > bond length. Before checking the distances between periodic images, > make sure that the solute not fragmented... > > Cheers, > > Tsjerk > > On Mon, Apr 30, 2012 at 4:38 PM, Thomas Evangelidis <teva...@gmail.com> wrote: >> >> Dear GROMACS users, >> >> I have a nanoparticle (perfect sphere) and want to enclose it into a rhombic >> dodecahedron. For this purpose I use the following command lines >> >> editconf_d4.5.5 -f nano.gro -bt dodecahedron -d 1 -c -o nano_box.gro >> grompp_d4.5.5 -f em.mdp -c nano_box.gro -p nano.top -o nano_box_EM.tpr >> mdrun_d4.5.5 -v -deffnm nano_box_EM >> >> echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f nano_box_EM.trr -s >> nano_box_EM.tpr -o nano_em_dodecahedron.xtc >> echo 2 | g_mindist_d4.5.5 -f nano_em_dodecahedron.xtc -s nano_box_EM.tpr -pi >> -od nano_mindist.xvg >> >> The first paradox is that the nanoparticle is fragmented in the dodecahedron >> representation for -d (editconf option) less that 1 nm. The second paradox >> is that the minimum distance between periodic images for -d 0.5, 1, 2, 3 is >> 0.183, 0.237, 4.171 and 6.167 nm respectively. The last two distances are >> close to the expected values but the first two are far from them. I would >> expect ~1 and ~2 nm for -d 0.5 and 1 respectively, since by definition with >> option -d and dodecahedron, the dimensions are set to the diameter of the >> system (largest distance between atoms) plus twice the speciï¬ ed distance. >> Can anyone explain what's happening? >> >> Thanks in advance. >> Thomas >> >> >> >> -- >> >> ====================================================================== >> >> Thomas Evangelidis >> >> PhD student >> >> Biomedical Research Foundation, Academy of Athens >> >> 4 Soranou Ephessiou , 115 27 Athens, Greece >> >> email: tev...@bioacademy.gr >> >>          teva...@gmail.com >> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> >> >> >> >> -- >> gmx-users mailing list   gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > > > ------------------------------ > > Message: 4 > Date: Tue, 01 May 2012 15:08:24 +0200 > From: Denis Kazakiewicz <d.kazakiew...@gmail.com> > Subject: [gmx-users] saltbridges newbie question > To: gmx-users@gromacs.org > Message-ID: <4f9fe048.9060...@gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello > Would you please give a hint or reference about how to interpret salt > bridge analysis graphs (output of g_saltbr command)? > Thank you > > Denis > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120501/e87c61e6/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 02 May 2012 00:19:44 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] disre and posres together? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f9ff100.2090...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > On 1/05/2012 4:58 PM, Banafsheh Mehrazma wrote: >> Dear all; >> I am wondering if we can use both disre and POSRES in .mdp file together? > > Yes, this is a routine procedure for equilibrating while preserving an > initial structure for some reason. > >> To be more perspective, is it correct to add all these below in the >> *.mdp file? >> .......................................... >> define= -DPOSRES >> disre = simple >> disre-weighting = equal >> disre-mixed = no >> disre-fc = 1000 >> disre-tau = 0 >> ......................................... >> > > That looks fine. > > Mark > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120502/c9a43d85/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Tue, 1 May 2012 11:50:55 -0500 > From: "Peter C. Lai" <p...@uab.edu> > Subject: Re: [gmx-users] saltbridges newbie question > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <20120501165054.gb94...@cesium.hyperfine.info> > Content-Type: text/plain; charset="us-ascii" > > If you use -sep it should just be distance over time of a given charged pair. > > The only functional difference between g_saltbr and g_dist is that g_saltbr > tries to be intelligent and preselects the pairs for you... > > On 2012-05-01 03:08:24PM +0200, Denis Kazakiewicz wrote: >> Hello >> Would you please give a hint or reference about how to interpret salt >> bridge analysis graphs (output of g_saltbr command)? >> Thank you >> >> Denis > >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > > > ------------------------------ > > Message: 7 > Date: Tue, 01 May 2012 19:02:30 +0200 > From: Denis Kazakiewicz <d.kazakiew...@gmail.com> > Subject: Re: [gmx-users] saltbridges newbie question > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fa01726.8030...@gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thank you indeed > Apologize for a silly question > On 01.05.2012 18:50, Peter C. Lai wrote: >> If you use -sep it should just be distance over time of a given charged pair. >> >> The only functional difference between g_saltbr and g_dist is that g_saltbr >> tries to be intelligent and preselects the pairs for you... >> >> On 2012-05-01 03:08:24PM +0200, Denis Kazakiewicz wrote: >>> Hello >>> Would you please give a hint or reference about how to interpret salt >>> bridge analysis graphs (output of g_saltbr command)? >>> Thank you >>> >>> Denis >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120501/e62649a1/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 97, Issue 6 > **************************************** -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists