Re: [gmx-users] distance restraint
Pathumwadee Intharathep wrote: Dear gmx's user, May I asked you some technicl Questions? Do you know how to make distance restraint in gromacs? what I did I have created file name "disre.itp" as shown below [ distance_restraints ] ; aiaj type index type low up1 up2 fac 489 1133 1 1 1 0.25 0.35 0.40 1.0 489 1164 1 2 1 0.25 0.35 0.40 1.0 490 1127 1 3 1 0.25 0.35 0.40 1.0 490 1167 1 4 1 0.25 0.35 0.40 1.0 in md.mdp file: title = M2_amand in POPC cpp = /lib/cpp constraints = all-bonds define = -DDISRES integrator = md dt = 0.002; ps ! nsteps = 50 ; total 1000 ps = 1 ns ! nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.2 pbc = xyz ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein POPC SOL Cl This is probably a bad idea... see http://wiki.gromacs.org/index.php/Thermostats tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 ; Energy monitoring energygrps = Protein POPC SOL Cl ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 310.0 disres = simple in topology.top file I added... ; Include distance restraint file #ifdef DISRES #include "disre.itp" #endif My questions are Q1:What is "column index" mean in disre.itp file? and how is it benefit? It's a label for the individual restraints, in case you need to refer to them. Guessing wildly, I suppose you might need labels to create sets for NMR time-averaged distance restraints. Q2:Where can I find in the output to make sure that my distances has already restrainted? The energy contributions from the restraints will be listed in the .log and the .edr files. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] cannot generate .top file
Kwee Hong wrote: Oo.. I'm so sorry for I'm not aware of this. But I'm really new to linux environment and don't really have a good mastering skill on the commandline that it works with. As you said that I'm not given the permission to write in that directory, sudo was the only thing that I can think of out from my knowledge. I don't really know how to do my work at the subdirectory of my hoe directory. OK. Just to prove I'm not an ornery old crank, here's a URL pointing out just some of the pitfalls of working as superuser... http://www.control-escape.com/linux/lx-postinstall.html#user In UNIX as in any field, the "Good Things To Do" are written in the blood and time of people who thought the above didn't apply to them! :-) And does the meaning of "adjust your environment variables to give you ready access to GROMACS stuff by using "source /path/to/GMXRC" using the path in which you installed the GROMACS binaries" requires me to make some changes in the source code or just by typing "source /path/to/GMXRC" at the terminal would have open the access for me in the directory? The latter. See http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation I'm sorry for my ignorance... I think I would better get some books on linux environment and read on it first. Great idea. Start with a web search - there's heaps of free UNIX tutorial material. Also, do some GROMACS tutorial material you can find on the web. These will give you more of a handle on how GROMACS things get done. Good luck! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] cannot generate .top file
Oo.. I'm so sorry for I'm not aware of this. But I'm really new to linux environment and don't really have a good mastering skill on the commandline that it works with. As you said that I'm not given the permission to write in that directory, sudo was the only thing that I can think of out from my knowledge. I don't really know how to do my work at the subdirectory of my hoe directory. And does the meaning of "adjust your environment variables to give you ready access to GROMACS stuff by using "source /path/to/GMXRC" using the path in which you installed the GROMACS binaries" requires me to make some changes in the source code or just by typing "source /path/to/GMXRC" at the terminal would have open the access for me in the directory? I'm sorry for my ignorance... I think I would better get some books on linux environment and read on it first. Joyce On Wed, Oct 29, 2008 at 12:11 PM, Mark Abraham <[EMAIL PROTECTED]>wrote: > Kwee Hong wrote: > >> Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the >> output files produced. I just added 'sudo' before ./pdb2gmx and it allows me >> to write in the directory. But unfortunately, this step seem does not work >> for ./gmxtest.pl. I'm having the same output even after i had added 'sudo' >> in front of it. >> > > If you do this kind of thing, your machine is a ticking time bomb. I gave > you good advice last time. I'm not going to give you more :-) > > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 search the archive at http://www.gromacs.org/search before posting! 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] distance restraint
Dear gmx's user, May I asked you some technicl Questions? Do you know how to make distance restraint in gromacs? what I did I have created file name "disre.itp" as shown below [ distance_restraints ] ; ai aj type index type low up1 up2 fac 489 1133 1 1 1 0.25 0.35 0.40 1.0 489 1164 1 2 1 0.25 0.35 0.40 1.0 490 1127 1 3 1 0.25 0.35 0.40 1.0 490 1167 1 4 1 0.25 0.35 0.40 1.0 in md.mdp file: title = M2_amand in POPC cpp = /lib/cpp constraints = all-bonds define = -DDISRES integrator = md dt = 0.002 ; ps ! nsteps = 50 ; total 1000 ps = 1 ns ! nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein POPC SOL Cl tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 ; Energy monitoring energygrps = Protein POPC SOL Cl ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 310.0 disres = simple in topology.top file I added... ; Include distance restraint file #ifdef DISRES #include "disre.itp" #endif My questions are Q1:What is "column index" mean in disre.itp file? and how is it benefit? Q2:Where can I find in the output to make sure that my distances has already restrainted? Thanks so much pathum ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] cannot generate .top file
Kwee Hong wrote: Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the output files produced. I just added 'sudo' before ./pdb2gmx and it allows me to write in the directory. But unfortunately, this step seem does not work for ./gmxtest.pl. I'm having the same output even after i had added 'sudo' in front of it. If you do this kind of thing, your machine is a ticking time bomb. I gave you good advice last time. I'm not going to give you more :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] cannot generate .top file
Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the output files produced. I just added 'sudo' before ./pdb2gmx and it allows me to write in the directory. But unfortunately, this step seem does not work for ./gmxtest.pl. I'm having the same output even after i had added 'sudo' in front of it. Joyce On Fri, Oct 24, 2008 at 8:52 PM, Mark Abraham <[EMAIL PROTECTED]>wrote: > Kwee Hong wrote: > >> Hi. >> I seem having some problem in running ./pdb2gmx. Here is the output file. >> Can you help me in giving me some idea to deal with this? >> >> bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro >> > > > >> --- >> Program pdb2gmx, VERSION 3.3.3 >> Source code file: futil.c, line: 313 >> >> File input/output error: >> 1aml.top >> --- >> > > This means it can't write 1aml.top, which likely means you don't have write > permission to the directory in which pdb2gmx resides. This is a Good Thing. > You should do daily work in a suitable subdirectory of (say) your home > directory, and adjust your environment variables to give you ready access to > GROMACS stuff by using "source /path/to/GMXRC" using the path in which you > installed the GROMACS binaries. I guess this is your attempted working > directory above. > > I seem to be having problem in running the test tun as well. Below is its >> output: >> bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl >> Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | >> kernel | pdb2gmx | all ] >> or: ./gmxtest.pl clean | refclean | dist >> > > Again this won't work in a directory in which you don't have write > permissions. The above message tells you that an empty command line isn't > acceptable to gmxtest.pl. *Technically* it ought to be acceptable per the > usage line, since square brackets denote optional things and |-symbols > denote a series of mutually-exclusive possibilities. I think the brackets > should be missing around "simple | complex | kernel | pdb2gmx | all". > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 search the archive at http://www.gromacs.org/search before posting! 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] Is there any realation between structure and RMSD?
Hi all I have simulated two systems(mutated and unmutated)of protein for 7ns and I plotted RMSD. here my doubt is that when I see these structures(superimpose)in VMD mutated final simulated structure with respective initial one drastic changes(means helix-coil and Beta-alpha transitions) but there is no change in unmutated structure with corresponding initial one. But when I plot RMSD, mutated structure showing low fluctuations(0.19nm)while unmutated(RMSD 0.3nm)high fluctuations. I have mentined RMSD command like this g_rms -f 7ns.xtc -s min.tpr -o 7ns_rmsd -pbc Selected c-alpha for both least square fit and RMSD calculation What I mean to say that the structure which shows changes(coil-helix and beta-alpha)it is supposed to has RMSD high viceversa but I am getting in opposite. Why its happening? Any suggestions would be appreciated Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] table use
Hi all users, When I input the mdrun -table table_nonbond.xvg it always shows that : Fatal error: Library file tablep.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Has anyone encountered the same problem? Can you share me your experience about how to solve it ? Thank you very much. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
Jochen Hub wrote: huan wrote: I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) Indeed; the g_energy output gives the x-axis as time... -Justin thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: From: Justin A. Lemkul <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: [EMAIL PROTECTED], "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 11:31 PM huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 . -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
huan wrote: > I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: > Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) > > thanks > > --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] density graph ( density vs time) >> To: [EMAIL PROTECTED], "Discussion list for GROMACS users" >> >> Date: Tuesday, October 28, 2008, 11:31 PM >> huan wrote: >>> Dear all, >>> >>> Previously i obtained a density (y-axis) versus box >> length (x axis) using g_density.. >>> So now i wonder is it there is another way that we can >> use other way to obtain a density (y axis) versus time >> length (x-axis). >> Use g_energy. >> >> -Justin >> >>> Thanks.. >>> >>> >>> --- On Tue, 10/28/08, Mark Abraham >> <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density >> vs time) To: "Discussion list for GROMACS users" >> Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: > Dear all gmx-users and developers. > > I wish to get a density graph with density >> versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't >> tell whether your problem is knowing what tool to use, how to use it, how to >> label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at >> http://www.gromacs.org/search before posting! 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 search the archive at >> http://www.gromacs.org/search before posting! >>> 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 >> -- >> >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
I used g_energy before but i just obtained density (y-axis) versus box length (x axis). now i wish to obtain density vs time thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph ( density vs time) > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Tuesday, October 28, 2008, 11:31 PM > huan wrote: > > Dear all, > > > > Previously i obtained a density (y-axis) versus box > length (x axis) using g_density.. > > > > So now i wonder is it there is another way that we can > use other way to obtain a density (y axis) versus time > length (x-axis). > > > > Use g_energy. > > -Justin > > > Thanks.. > > > > > > --- On Tue, 10/28/08, Mark Abraham > <[EMAIL PROTECTED]> wrote: > > > >> From: Mark Abraham <[EMAIL PROTECTED]> > >> Subject: Re: [gmx-users] density graph ( density > vs time) > >> To: "Discussion list for GROMACS users" > > >> Date: Tuesday, October 28, 2008, 4:46 PM > >> huan wrote: > >>> Dear all gmx-users and developers. > >>> > >>> I wish to get a density graph with density > versus time > >> instead of nm, so how can i obtained this? > >> > >> Please ask a more specific question. We can't > tell > >> whether your problem > >> is knowing what tool to use, how to use it, how to > label > >> axes of plots > >> or something else. > >> > >> Mark > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > http://www.gromacs.org/search > >> before posting! > >> 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 search the archive at > http://www.gromacs.org/search before posting! > > 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 > > > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Thanks.. --- On Tue, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph ( density vs time) > To: "Discussion list for GROMACS users" > Date: Tuesday, October 28, 2008, 4:46 PM > huan wrote: > > Dear all gmx-users and developers. > > > > I wish to get a density graph with density versus time > instead of nm, so how can i obtained this? > > Please ask a more specific question. We can't tell > whether your problem > is knowing what tool to use, how to use it, how to label > axes of plots > or something else. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > 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 search the archive at http://www.gromacs.org/search before posting! 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] Adding Na ions to DPPG
On Mon, Oct 27, 2008 at 10:21 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Peyman Yamin wrote: > >> On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: >> >>> Peyman Yamin wrote: >>> On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. >>> Well that makes more sense. I'm assuming you have a DPPG bilayer with >>> solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer >>> in solution, just use genion; you can even specify exactly how many Na+ >>> you >>> want using -np. >>> >>> If the topology organization is confusing you, refer to Chapter 5 of the >>> manual. If you make a .top for DPPG, you can specify: >>> >>> [ molecules ] >>> DPPGx >>> NA+ 1 (or whatever) >>> >>> after including the appropriate force field call and ions.itp; the >>> parameters for all atom types are taken from these files. >>> >> >> Well this looks great! I simulate one single DPPG in solvent. and you >> know, this Na+ is not in solvent but a part of DPPG. So you mean I just make >> a DPPG with an O which has no H so is minus and then use genion to add Na? >> will it place the Na aroung O hopefully? I think if I put no H arounf O the >> prodrg will force me to have it! so I should delete it and replace it with >> Na? or I should never use the word "replace" at all??? >> >> > Well, the Na+ may be associated with DPPG electrostatically, but they are > still distinct chemical entities. You can have a DPPG that has a net -1 > charge; certainly all chemical species are not net neutral! Indeed, genion > will place Na+ in whatever solvent you choose, but may not necessarily be > bound to DPPG. Some simulation may show the association, however. > Yes, keep the DPPG. The charge distribution around anionic lipid has been studied. http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO0001010303810301&idtype=cvips&gifs=yes > > And no, don't replace any part of your DPPG. Because then you don't really > have DPPG any more do you? > > -Justin > > > Thanks again ;) >> Peyman >> >> -Justin >>> >>> Peyman Yamin wrote: > >> Dear GMX users, >> >> I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the >> structure with the Na replaced with O. I get a .top with this from >> prodrg and try to add the Na manually at the right place by removing >> the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1.I >> have a problem: >> > Are you trying to replace the O in DPPG with Na+? Or are you simply > trying to add ions to the surrounding solvent (water)? If you just > need > ions in the solvent, use genion; you don't have to do it manually. > > * In .top file, as far as I can understand, I should just replace OA >> with NA+ and set the mass and charge. >> DPPG has a centre: [ O-P(O)=O ] - >> The Na+ should be around this with +1 charge. >> should I put charge +1 ? >> > Again, I'm not clear on what you're trying to accomplish. If you > replace one of these oxygen atoms, you will likely not have an integer > charge within the DPPG molecule itself. > > * which parameters should I place in the top as the Na+ is not >> bonding. >> I need LJ and Coulomb params. I have C6 and C12 them from >> ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the >> top file. What should I insert manually in top file at all? >> > Simply #include "ffG43a1.itp" at the top of your .top file; it will > include nonbonded and bonded parameters for all the atoms in the > system. > > -Justin > > Thanks in advance for the time, >> I've been away for some time from GMX and might sound >> >> Cheers, >> Peyman >> > >> > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -- Best wishes, Myunggi Yi == KLB 419 Institute of Molecular Biophysics Florida State University Tallahasse
Re: [gmx-users] dielectric coffiecient
shahrbanoo karbalaee wrote: Deat justin thanks for your help. I delete cl- from (peptide,tfe ,water) in my system and I see about his charge not get message. when I add tfe in peptide (pdb2gmx -f name.pdb -ter -ignh )the lysin amino acid is protonated (2 lysin).another charge aminoacid is D,E.do you think it related to adding tfe to system.because my peptide charge is +1.please advise me. and another ,do I need to define e (dielectric E) for water and tfe in my mdp files ?or has the program default? If your peptide has a net charge of +1, then you need a counterion to neutralize the charge. But I'm confused. If you have 2 Lys and an Asp and Glu, then the net charge should be 0, unless you've done something strange with your termini. There is no need to set a dielectric, at least not with PME for electrostatics. If you're using reaction field, then you would specify a dielectric beyond a certain cut-off. -Justin best -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Re: dihedrals again
Remark: if I change that dihedral with -CHCH2 CH CBgd_17, that it gives again 2 9 10 11 , but this time with gd_17, as it should do. But why it does not work with the other definition? Does it have to do with the fact that in the dihedral I have atoms belonging to 3 residues? And are the 2 definitions (with +CH2 and CB at the end) equivalent, taking in acount that we define also an improper of type gi_2 around the CH atom? Cheers, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] dihedrals again
Hi all, I did some work on thise dihedrals for polystyrene, and I simplified my version now, using also the inspiration from PHE residue. My problem now is that for the dihedral around the CH2-CH bond in the inner monomer (PS thus) I define in the rtp -CH CH2 CH +CH2gd_17 but in the top fileinstead of 2 9 10 17 gd_17 I get this: 2 9 10 11 (without any parameter). This make me think that pdb2gmx does not count the dihedral as I defined it (why?) but puts a "default" dihedral there, without any parameter. I am right? What would be a solution for that? My dihedrals are now defined as follows (it helps if you really draw the molecule): the entries in the rtp file for first (PS1), inner (PS) and last (PSN) monomer: [PS1] [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_17 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 [PS] [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_17 -CH CH2 CH +CH2gd_17 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 [PSN] [dihedrals] ;in the chain - 3-fold (n=3) -CH CH2 CH CH3 gd_17 ;around CH-CB - 2-fold (n=2) CH2 CH CB CG5 gd_1 The results for trimer in the top file. [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 8 1gd_1 1 2 910 1gd_17 2 91011 1 9101116 1gd_1 9101718 1gd_17 10171825 1gd_17 17181924 1gd_1 Best regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] dielectric coffiecient
Deat justin thanks for your help. I delete cl- from (peptide,tfe ,water) in my system and I see about his charge not get message. when I add tfe in peptide (pdb2gmx -f name.pdb -ter -ignh )the lysin amino acid is protonated (2 lysin).another charge aminoacid is D,E.do you think it related to adding tfe to system.because my peptide charge is +1.please advise me. and another ,do I need to define e (dielectric E) for water and tfe in my mdp files ?or has the program default? best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
huan wrote: > Dear all gmx-users and developers. > > I wish to get a density graph with density versus time instead of nm, so how > can i obtained this? You could extract the box vectors with g_energy and compute the density from the volume. Best, Jochen > > Thanks. > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] density graph ( density vs time)
Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] empty velocity *.xvg file from g_traj
Inon Sharony wrote: > > Good morning! > > Firstly, I'd like to thank congratulate everyone involved for ver 4.0 > > > Now for business: > > I'm getting empty *.xvg files from g_traj... this doesn't always > happen, and I can't find what I'm doing differently... I'm running > version 3.3.3 on Ubuntu: > > > > > grompp_d -f eq -c b4eq -n -t > mdrun_d -c b4md -v > > grompp_d -f md -c b4md -n -t > mdrun_d -c md -v > > g_traj_d -n -ox x_ndxgrp1 -ov v_ndxgrp1 > > By default, g_traj reads the traj,xtc (check g_traj -h) which does not contain velocities. Have you tried g_traj_d -f traj.trr ? Jochen > > > gives me two *.xvg files: > the x_ndxgrp1 file is fine, but v_ndxgrp1 has an xmgrace formatting > header, and then no data afterward. This formatting information agrees > with the number of atoms in the group ndxgrp1. > > what am I doing wrong? > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] empty velocity *.xvg file from g_traj
Good morning! Firstly, I'd like to thank congratulate everyone involved for ver 4.0 Now for business: I'm getting empty *.xvg files from g_traj... this doesn't always happen, and I can't find what I'm doing differently... I'm running version 3.3.3 on Ubuntu: grompp_d -f eq -c b4eq -n -t mdrun_d -c b4md -v grompp_d -f md -c b4md -n -t mdrun_d -c md -v g_traj_d -n -ox x_ndxgrp1 -ov v_ndxgrp1 gives me two *.xvg files: the x_ndxgrp1 file is fine, but v_ndxgrp1 has an xmgrace formatting header, and then no data afterward. This formatting information agrees with the number of atoms in the group ndxgrp1. what am I doing wrong? -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
