Re: [gmx-users] CPMD- QM MM simulation

2008-09-08 Thread Gerrit Groenhof
Message: 1 Date: Fri, 5 Sep 2008 15:48:12 -0700 From: "Chih-Ying Lin" <[EMAIL PROTECTED]> Subject: [gmx-users] CPMD- QM MM simulation To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi I read some papers, which the authors use CPMD

[gmx-users] Re: trr file format

2008-09-08 Thread Vitaly Chaban
gurgo> Vitaly Chaban wrote: >> Hello, >> >> Where can I read about the exact format of the TRR and XTC files. I >> mean the width and type of every field in the binary trajectory file. >> >> I see read_'next_frame(status,&fr)' function in 'template.c'. But >> where is this fuction defined? >> Sor

Re: [gmx-users] Software for ESP fitting

2008-09-08 Thread David van der Spoel
Vasilii Artyukhov wrote: Hi gmx-users, Sorry for a not-strictly-GROMACS-related question, but could someone suggest a program I could use to fit atomic charges to quantum chemistry results? antechamber. Thanks in advance, Vasilii -

Re: [gmx-users] Fatel error in simulated annealing

2008-09-08 Thread Justin A. Lemkul
ravi sharma wrote: Thanks justin, but how can identify these groups, i am using fedora core 8, also Thanks for the Tc-grps, What groups are you talking about, tc-grps? Please be more specific. -Justin regards, --- On *Sun,

Re: [gmx-users] Software for ESP fitting

2008-09-08 Thread Vasilii Artyukhov
2008/9/8 David van der Spoel <[EMAIL PROTECTED]> > Vasilii Artyukhov wrote: > >> Hi gmx-users, >> >> Sorry for a not-strictly-GROMACS-related question, but could someone >> suggest a program I could use to fit atomic charges to quantum chemistry >> results? >> >> antechamber. Thanks for a quick

Re: [gmx-users] force field for boron-nitride nanotube

2008-09-08 Thread Justin A. Lemkul
jj beh wrote: Dear all user How can I have a force field for simulation of boron-nitride nanotube? Has anything like that ever been simulated? If it hasn't, there may not be paramteers for such a species. I don't believe boron exists as an atom type in any of the force fields provided b

[gmx-users] Re[2]: trr file format

2008-09-08 Thread Vitaly Chaban
gurgo>> Vitaly Chaban wrote: >>> Hello, >>> >>> Where can I read about the exact format of the TRR and XTC files. I >>> mean the width and type of every field in the binary trajectory file. >>> >>> I see read_'next_frame(status,&fr)' function in 'template.c'. But >>> where is this fuction define

[gmx-users] force field for boron-nitride nanotube

2008-09-08 Thread jj beh
Dear all user How can I have a force field for simulation of boron-nitride nanotube? The pdb file of nanotube is as follow: HETATM1 N1 UNK 1 1.597 0.000 -5.015 1.00 0.00 N HETATM2 N2 UNK 1 1.129 1.129 -2.870 1.00 0.00 N HETATM3 B3 UNK 1 1.1

[gmx-users] Re: force field for boron-nitride nanotube

2008-09-08 Thread Vitaly Chaban
Of course, there exist a bunch of works simulating B-N NTs. See papers. PDB file isn't enough to make a topology for gromacs. gurgo> Has anything like that ever been simulated? If it hasn't, there may not be gurgo> paramteers for such a species. I don't believe boron exists as an atom type in

[gmx-users] sn1 and sn2 chains of popc

2008-09-08 Thread minnale
Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2? Thanks for y

[gmx-users] manipulation of trajectory data

2008-09-08 Thread Inon Sharony
Hello GROMACS users! I would like to preform arithmetic operations on trajectories which are output from GROMACS simulations (e.g., to multiply the velocity of atom 1 by that of atom 2, and average over time). I have read in the mailing lists references to g_traj and other functions, but think

Re: [gmx-users] Fatel error in simulated annealing

2008-09-08 Thread Justin A. Lemkul
ravi sharma wrote: hi you have written that in my file there are some trailing characters, how can identify these characters ?? You can see them in the vi editor. -Justin ;simulated annealing > annealing = single^M > annealing_npoints = 5 ^M > annealing_time = 2 500 100

[gmx-users] Software for ESP fitting

2008-09-08 Thread Vasilii Artyukhov
Hi gmx-users, Sorry for a not-strictly-GROMACS-related question, but could someone suggest a program I could use to fit atomic charges to quantum chemistry results? Thanks in advance, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://ww

Re: [gmx-users] CPMD- QM MM simulation

2008-09-08 Thread Christian Seifert
Hi. Anyway, it would be nice to have a structured manual for the GMX/CPMD interface. The website http://www.tougaloo.edu/research/qmmm has just a few basic information and further information in this mailing list under http://www.gromacs.org/pipermail/gmx-users/2006-June/022329.html are not that e

Re: Re: [gmx-users] sn1 and sn2 chains of popc

2008-09-08 Thread minnale
Thanks Justin for your reply you mean to say that C32 of glycerol involves in the palimotyl chain formation so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl chain formation so call as sn2. Am I correct? Thanks in advance. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : > > >m

Re: [gmx-users] sn1 and sn2 chains of popc

2008-09-08 Thread Justin A. Lemkul
minnale wrote: Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as

Re: [gmx-users] sn1 and sn2 chains of popc

2008-09-08 Thread Justin A. Lemkul
minnale wrote: Thanks Justin for your reply you mean to say that C32 of glycerol involves in the palimotyl chain formation so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl chain formation so call as sn2. Am I correct? More or less, let's just get a few things straig

[gmx-users] Re: trr file format

2008-09-08 Thread Vitaly Chaban
Thank you! After a day of searches I found the function body I wanted. :) gurgo> Hello, gurgo> if you have problems, finding appropiate header files for the gurgo> functions of gmx, you can perhaps use a development environment like gurgo> Eclipse, Source-Navigator, KDevelop, Anjuta depending

[gmx-users] RE: manipulation of trajectory data

2008-09-08 Thread Vitaly Chaban
gurgo> If anyone has a simpler example along the lines of my interests, gurgo> please send me it! and to me... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

Re: [gmx-users] RE: manipulation of trajectory data

2008-09-08 Thread Omer Markovitch
to me too. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 16:30, Vitaly Chaban <[EMAIL PROTECTED]>wrote: > gurgo> If anyone has a simpler example along the lines of my interests, > gurgo> please send me it! > > >

[gmx-users] Re[2]: manipulation of trajectory data

2008-09-08 Thread Vitaly Chaban
OM> to me too. OM>  OM> Koby Levy research group, OM> Weizmann Institute of Science.  OM> http://www.weizmann.ac.il/sb/faculty_pages/Levy/ It sounds like an epidemic of analyzing gromacs trajectories. :) --  Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4,

[gmx-users] installation problem: undefined symbols: _gmx_fft_(init_)3d_real

2008-09-08 Thread Ervasti, H. (Henri)
Dear all, I would like to ask you help on an installation issue of GROMACS. When I am running ''make'' after configuring GROMACS, I get the following error: /usr/libexec/gcc/i686-apple-darwin8/4.2.1/ld: undefined symbols: _gmx_fft_3d_real _gmx_fft_init_3d_real Collect2: ld returned 1 exit

[gmx-users] Re: Re[6]: Using Morse potentials with ENCAD force field

2008-09-08 Thread Andy Shelley
I am trying to make a radial temperature profile of a given thickness. I originally used the confout.gro file containing the final output of velocity and position of each atom to calculate the temperature from the velocity but would like to take time averages now. Andy On Sat, Sep 6, 2008 at 4:21

Re: [gmx-users] Fatel error in simulated annealing

2008-09-08 Thread Justin A. Lemkul
ravi sharma wrote: Hello justin, whether i do correct my md.mdp by vi editor but still it was giving error well i removed all those groups which coupling to thermostat now its working (NA+ HEME SOL) I guess I hadn't even considered that. If you're doing simulated annealing, and progres

[gmx-users] optimizing the mailing list

2008-09-08 Thread chris . neale
I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow submitters to flag messages as belonging to some particular topic(s). e.g. "program crash" "force fields" "protein" "free energy" "coarse graining" "lipids and detergents" "unknown" etc.

[gmx-users] How to convert gromacs traj file(.xtc) to amber traj file?

2008-09-08 Thread ranqi zhu
Hi, Everyone, I just want to use the clustering tool in amber which only take trj file. Thanks -Ranqi _ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spac

[gmx-users] RE: optimizing the mailing list

2008-09-08 Thread Vitaly Chaban
it's called internet forum... :) > I suggest that we consider ways in which the mailing list can be > optimized. My initial thought is to allow submitters to flag messages > as belonging to some particular topic(s). > > e.g. > "program crash" > "force fields" > "protein" > "free energy" > "coar

Re: [gmx-users] RE: optimizing the mailing list

2008-09-08 Thread David van der Spoel
Vitaly Chaban wrote: it's called internet forum... :) we've had this discussion before. On a forum many of the hardcore gromacs people (like me) would probably not respond anymore. I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow su

[gmx-users] still some problems with HP-UX... grompp acting weird

2008-09-08 Thread Christopher Daub
Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this

Re: [gmx-users] RE: optimizing the mailing list

2008-09-08 Thread Omer Markovitch
Using emails, this might be done "manually" - each user will add to the TOPIC something like: "tag install", etc`. Then each user could define his own rule, in his personal email account, how to deal with messages that contain "tag xxx" & "gromacs" in the topic. Just a thought... Omer. Koby Levy r

Re: [gmx-users] How to convert gromacs traj file(.xtc) to amber traj file?

2008-09-08 Thread Omer Markovitch
Are you sure this will be done automaticaly if you'll procide gromacs with an output file called filename.trj? There is also the option of converting into PDB: "trjconv -f traj.xtc -o trajtraj.pdb -s coordinates.gro". omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizma

Re: Re: [gmx-users] sn1 and sn2 chains of popc

2008-09-08 Thread minnale
Thanks alot Justin for your detailed explanation. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : > > >minnale wrote: >>Thanks Justin for your reply >>you mean to say that C32 of glycerol involves in the palimotyl chain >>formation so call as sn1 chain similarly C12,C13 of glycerol involves in the

Re: [gmx-users] still some problems with HP-UX... grompp acting weird

2008-09-08 Thread David van der Spoel
Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine u

Re: [gmx-users] How to convert gromacs traj file(.xtc) to amber traj file?

2008-09-08 Thread David van der Spoel
Omer Markovitch wrote: Are you sure this will be done automaticaly if you'll procide gromacs with an output file called filename.trj? There is also the option of converting into PDB: "trjconv -f traj.xtc -o trajtraj.pdb -s coordinates.gro". omer. try trjconv -o blabla.g87 -f something Kob

[gmx-users] (no subject)

2008-09-08 Thread minnale
Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ gmx-users mailing list

[gmx-users] conversion?

2008-09-08 Thread minnale
Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ gmx-users mailing list