Re: [gmx-users] radial densities
Can't think of a current program that does this. One option is to: 1. Use g_sdf from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001786.html 1b. With the bug fix from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001791.html BUG: line 216 of 298 should have divided Y and Z by "bohr", not just X as was previously posted. The correct line is: fprintf(flp,"%5d%12.6f%12.6f%12.6f\n",nidxp,(MINBIN[XX]+(minx+iIGNOREOUTER) *rBINWIDTH)*10./bohr,(MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr); 1c. With the fixed order of alignment prior to running g_sdf from here: http://www.gromacs.org/pipermail/gmx-users/2006-August/023549.html trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans This will give you the spatial distribution function... not quite what you want. However, you could easily write a bash script that converted this spatial distribution function into an all-helix radial distribution function (if I am correct that you intend to derive a single plot with radial distance on the x axis and a density-given-x over the y axis). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA
Yes, I'm using Cut-off. And the Error is reproducable. I'll post the bug report. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David van der Spoel wrote: Maik Goette wrote: Hi I just observed very strange results with my system (around 700 atoms in vacuum), when doing normal mode analysis. The eigenvalues were all negative. I then took an old nma-system from Bert de Groot and did the nma with 3.3.1 on it and observed the same strange results. After that I tried 3.2.1 on that system and the results were quite similar to the ones Bert got with 3.1.4. My vacuum-system yields (more or less) correct (not nice) results on the first look. Is there something new to obey in 3.3.1 what isn't mentioned in the manual (3.11 NMA)? If not, I would think, there's a bug. Any suggestions? Regards Are you using cut-offs? In that case gromacs uses a different algorithm now, which might cause the problem. Anyway if you have a reproducible problem please report a bugzilla and upload the necessary files. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv for hexa-meric protein
Hi I simulate a hexa-meric protein (443*6=2658 residues with about 9 water) Especially, I'm interested in water behavior around the protein. The 1ns simulation is finished normally, but trjconv produces abnormal structure. For example, the protein go outside my waterbox, water molecules are diverse abnormally...etc. I try various options: trjconv -s full.tpr -f full.trr -o full.xtc -pbc nojump trjconv -s full.tpr -f full.trr -o full.xtc -pbc cluster trjconv -s full.tpr -f full.trr -o full.xtc -fit rot (select 1(thus protein) for fitting group) And, I watch full.xtc using VMD, but they are strange in all cases. For your information, I use cubic periodic boundary condition. Please suggest me. Greetings, Tomoshi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] change number of processors after tpbconv
hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] change number of processors after tpbconv
Carsten Baldauf wrote: hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php No, you have to use grompp -t -e -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OPLS + ffgmx
Hi Mark and Chris, Thanks a lot to both of you for going through my query, for suggesting the positive and negative points of this procedure. I will think and then decide how to go about it. I am really thankful to Chris for the detailed suggestion regarding the procedure. I will come back to you later as I go about it. Thanking you all again, Regards, Alok. - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, September 06, 2006 7:47 AM Subject: Re: [gmx-users] OPLS + ffgmx Hi all, I am trying to do a membrane protein simulation. I want to use OPLS - AA force field for protein and ffgmx (modified ffgmx force filed with lipid parameters from user contribution section ) force field for POPE lipids. Is it is possible and advisable to use two different force fields for protein and lipids? In general, this way madness lies. Force fields are mathematical constructs that are optimized to approximately reproduce some experimental properties *in cooperation with itself*. There is no reason to expect that force field parameters for "bond strength" have any great correlation with an experimentally determined bond strength, and thus to have no correlation with a "bond strength" from another force field. Accordingly there's no reason to expect that a mixture of parts of different force fields will work well together. It's somewhat like taking half of a soccer team and half of a gridiron team and expecting them to be able to play rugby together. Or else, Is there any all atom force field availble for lipid molecules which I can use? CHARMM parameter sets optimized for combined protein & lipid calculations exist. Simplest would then be to use CHARMM or NAMD. If you want to use GROMACS, you can get such a force field, use my scripts available here http://www.gromacs.org/contributed_by_users/task,doc_details/gid,59/ to convert them to gromacs format, obtain some .rtp files elsewhere, test carefully, and simulate to your heart's content. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] change number of processors after tpbconv
thank you// David van der Spoel wrote: Carsten Baldauf wrote: hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php No, you have to use grompp -t -e ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about gromacs
Hello, everyone: Would you please tell me that whether Gromacs can be used to do Molecular Dynamics studies for Polymer like PVC or PET? Thanks a lot. dai0601 2006-09-07 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulation problem with extended membrane system!
Hi ChrisThank you for your suggestions!These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out. I'm trying to use the method you suggested, I searched the list, find there is some scripts offered by other users, but I'm new to Linux and gromacs, I've got no idea which one to use and how to use it. So would you please send me a sample? Thank you very much for your helpXin LiuOn 9/5/06, [EMAIL PROTECTED] < [EMAIL PROTECTED]> wrote:It is unclear why your second method works for you. However, given that it does, just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3and then use your own script to remove any spc waters that were put inside themembrane and modify the nubers in your topology file accordingly. I imagine that your first attempt didn't work since an entire dppc molecule isremoved upon a single collision and this will lead to "holes" in your membranethat will quickly fill with water. Of course this should also have happened in your second attempt... I am not sure what was different there.You need semiisotropic pressure coupling and you need to stop every once and awhile and remove any water molecules that are inside the membrane. Note that isotropic Pcoupling in a membrane system (as you have been doing) has thepotential to provide a surface tension (or the opposite) that you have not beenintentionally including and so you can expect your membrane to behave differently. Chris.___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
