Re: [gmx-users] g_sas Vdwradii.dat
maite lopez cabezas wrote: Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité Search the literature for papers about this. I forgot where the current values come from, it could well be that they the Eisenhaber paper. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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] analysis of different groups with g_energy
Peyman Yamin wrote: Hi again, Now I remember! some old g_energy let me use numbers as the input for the terms I wanted...! Yeah, it changed going from 3.3 to 3.3.1, IIRC. This allowed for scripts to be much more general, since the numbers used to change for different simulation types. As you say, it looks like the total energy for different groups is not calculated. So I should somehow do it myself? If yes, I don't even know where I should get the terms I should add together from? I think I'd need all bonding and nonbonding interactions! or I should even calculate them? See my previous email... the most reliable way is to invoke cpp on your .top file to do all the #includes, and then to go through it with a text editor and zero out everything that you feel should be zeroed out. You'll probably have to halve all of the non-bonded terms yourself by hand after the mdrun -rerun. I can't also find what SR and LR and 14 mean in energy terms...! short range, long range and 1-4 interactions. See early chapters of GROMACS manual for details. 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] analysis of different groups with g_energy
Peyman Yamin wrote: Thanks! I had somewhere in my mind a memory of seeing an interactive g_energy some time ago, but it could be another version of it or that place in my mind would need a defragmentation! comments helped indeed anyway. If group X is one molecule, you would know from it's energy, i.e. the sum of interactions its atoms have with themself and with the surrounding solvent, a plenty of useful things. It could, if analysed with an eye on physicochemical nature of interactions and the resulting conformers, could give neat insights in some cases. e.g. how would one find some attractors about a certain arbitrarily defined size-related property, in terms of stability? I thought if molecule X is tending to have some conformer with the least energy in medium A, it would also be tending to have an alike conformer in some other medium of the same nature to the first one. In general, you can't just ignore entropic considerations here - that's one reason for doing condensed-phase MD, rather than vacuum calculations of some sort. MM forcefields are typically parameterized to reproduce certain physical or quantum chemical computational observables. Unless you can show a direct relationship between some of these and your property of interest, then you're on very shaky ground using the MM forcefield. This is what I think, and, you might want to correct me of course. But what I don't know now is if the tot-energy output from g_energy when one chooses a certain molecule, is actually what I think it is, or it's calculated in another way? How would I know? "Total energy" in g_energy and the .log file is for the whole system. An mdrun -rerun with a topology that's had most of its contributions zero-ed out is one way to get your single-molecule total energy. 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] how to distancing the counter ions from the protein?
jayant james wrote: Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity to the protein. Is it possible to keep them away from the protein because I do not want them so close !! What about your system makes "close proximity" seem wrong? 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] analysis of different groups with g_energy
Hi again, Now I remember! some old g_energy let me use numbers as the input for the terms I wanted...! As you say, it looks like the total energy for different groups is not calculated. So I should somehow do it myself? If yes, I don't even know where I should get the terms I should add together from? I think I'd need all bonding and nonbonding interactions! or I should even calculate them? I can't also find what SR and LR and 14 mean in energy terms...! Would greatly appreciate any suggestion, Peyman On Monday 09 June 2008 18:27, Mark Abraham wrote: > Peyman Yamin wrote: > > On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: > > > > Well, ofcourse I did! otherwise I wouldn't expect any program to know > > them by itself! the problem is that I say: > > Well, there's a lesson here. You should spell out all relevant data - > like your usage of energy groups in your run input file and your full > observations of g_energy the first time. We don't read minds here, and > Justin's assumption of your probable failure to plan for your own > analysis seems to be borne out by the way most new people approach MD > simulations :-) > > > # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o > > tot_ener > > > > and I get: > > > > > > Opened ../ener.edr as single precision energy file > > > > Select the terms you want from the following list > > - > > Angle Proper-Dih. Improper-Dih. LJ-14 > > Coulomb-14 LJ-(SR) Coulomb-(SR)Coulomb-(LR) > > RF-excl.Potential Kinetic-En. Total-Energy > > Temperature Pressure-(bar) Box-X Box-Y > > Box-Z Volume Density-(SI)pV > > Vir-XX Vir-XY Vir-XZ Vir-YX > > Vir-YY Vir-YZ Vir-ZX Vir-ZY > > Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) > > Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) > > Pres-ZY-(bar) Pres-ZZ-(bar) #Surf*SurfTen Pcoupl-Mu-XX > > Pcoupl-Mu-YYPcoupl-Mu-ZZMu-XMu-Y > > Mu-ZCoul-SR:OCT-OCT LJ-SR:OCT-OCT Coul-LR:OCT-OCT > > Coul-14:OCT-OCT LJ-14:OCT-OCT Coul-SR:OCT-TX1 LJ-SR:OCT-TX1 > > Coul-LR:OCT-TX1 Coul-14:OCT-TX1 LJ-14:OCT-TX1 Coul-SR:TX1-TX1 > > LJ-SR:TX1-TX1 Coul-LR:TX1-TX1 Coul-14:TX1-TX1 LJ-14:TX1-TX1 > > T-OCT T-TX1 Lamb-OCTLamb-TX1 > > > > without any notification for choosing a group. > > Actually, that's all the notification you get. You can type a > newline-delimited list of the energy terms you'd like, and follow it > with a blank line and g_energy will produce your output. You may also > like to consult > http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive > > Note, however, that "total energy of group X" is not available. That's > because it isn't calculated, and in the vast majority of cases it > wouldn't mean anything anyway. You can see a breakdown of the nonbonded > interactions there, however. > > > On the other hand, for instance > > when I say: > > > > # g_gyrate -f out.xtc -s ../25ns.tpr > > > > I get, in a beautiful way: > > > > Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) > > Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) > > Opening library > > file /apps/GMX/331-intel64-intelmpi-wc/share/gromacs/top/aminoacids.dat > > Group 0 ( System) has 24476 elements > > Group 1 ( TX1) has46 elements > > Group 2 ( OCT) has 24430 elements > > Select a group: > > > > Now I don't know why I don't get the same behaviour with g_energy, if at > > all I should expect such a thing! > > It's inconsistent, but probably reflects that a different person wrote > the two programs. > > 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 -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik University of Erlangen Egerlandstr. 3, 91058 Erlangen, Germany peyman.yamin AT cbi.uni-erlangen.de ___ 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] how to distancing the counter ions from the protein?
Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity to the protein. Is it possible to keep them away from the protein because I do not want them so close !! Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ 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] analysis of different groups with g_energy
Thanks! I had somewhere in my mind a memory of seeing an interactive g_energy some time ago, but it could be another version of it or that place in my mind would need a defragmentation! comments helped indeed anyway. If group X is one molecule, you would know from it's energy, i.e. the sum of interactions its atoms have with themself and with the surrounding solvent, a plenty of useful things. It could, if analysed with an eye on physicochemical nature of interactions and the resulting conformers, could give neat insights in some cases. e.g. how would one find some attractors about a certain arbitrarily defined size-related property, in terms of stability? I thought if molecule X is tending to have some conformer with the least energy in medium A, it would also be tending to have an alike conformer in some other medium of the same nature to the first one. This is what I think, and, you might want to correct me of course. But what I don't know now is if the tot-energy output from g_energy when one chooses a certain molecule, is actually what I think it is, or it's calculated in another way? How would I know? Regards, Peyman On Monday 09 June 2008 18:27, Mark Abraham wrote: > Peyman Yamin wrote: > > On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: > > > > Well, ofcourse I did! otherwise I wouldn't expect any program to know > > them by itself! the problem is that I say: > > Well, there's a lesson here. You should spell out all relevant data - > like your usage of energy groups in your run input file and your full > observations of g_energy the first time. We don't read minds here, and > Justin's assumption of your probable failure to plan for your own > analysis seems to be borne out by the way most new people approach MD > simulations :-) > > > # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o > > tot_ener > > > > and I get: > > > > > > Opened ../ener.edr as single precision energy file > > > > Select the terms you want from the following list > > - > > Angle Proper-Dih. Improper-Dih. LJ-14 > > Coulomb-14 LJ-(SR) Coulomb-(SR)Coulomb-(LR) > > RF-excl.Potential Kinetic-En. Total-Energy > > Temperature Pressure-(bar) Box-X Box-Y > > Box-Z Volume Density-(SI)pV > > Vir-XX Vir-XY Vir-XZ Vir-YX > > Vir-YY Vir-YZ Vir-ZX Vir-ZY > > Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) > > Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) > > Pres-ZY-(bar) Pres-ZZ-(bar) #Surf*SurfTen Pcoupl-Mu-XX > > Pcoupl-Mu-YYPcoupl-Mu-ZZMu-XMu-Y > > Mu-ZCoul-SR:OCT-OCT LJ-SR:OCT-OCT Coul-LR:OCT-OCT > > Coul-14:OCT-OCT LJ-14:OCT-OCT Coul-SR:OCT-TX1 LJ-SR:OCT-TX1 > > Coul-LR:OCT-TX1 Coul-14:OCT-TX1 LJ-14:OCT-TX1 Coul-SR:TX1-TX1 > > LJ-SR:TX1-TX1 Coul-LR:TX1-TX1 Coul-14:TX1-TX1 LJ-14:TX1-TX1 > > T-OCT T-TX1 Lamb-OCTLamb-TX1 > > > > without any notification for choosing a group. > > Actually, that's all the notification you get. You can type a > newline-delimited list of the energy terms you'd like, and follow it > with a blank line and g_energy will produce your output. You may also > like to consult > http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive > > Note, however, that "total energy of group X" is not available. That's > because it isn't calculated, and in the vast majority of cases it > wouldn't mean anything anyway. You can see a breakdown of the nonbonded > interactions there, however. > > > On the other hand, for instance > > when I say: > > > > # g_gyrate -f out.xtc -s ../25ns.tpr > > > > I get, in a beautiful way: > > > > Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) > > Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) > > Opening library > > file /apps/GMX/331-intel64-intelmpi-wc/share/gromacs/top/aminoacids.dat > > Group 0 ( System) has 24476 elements > > Group 1 ( TX1) has46 elements > > Group 2 ( OCT) has 24430 elements > > Select a group: > > > > Now I don't know why I don't get the same behaviour with g_energy, if at > > all I should expect such a thing! > > It's inconsistent, but probably reflects that a different person wrote > the two programs. > > 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 -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik University of Erlangen Egerlandstr. 3, 91058 Erlangen, Germany peyman.yamin AT cbi.uni-er
Re: [gmx-users] g_sas Vdwradii.dat
Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité On Sat, Jun 7, 2008 at 4:50 PM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Xavier Periole wrote: > >> On Sat, 07 Jun 2008 22:32:29 +0200 >> "Xavier Periole" <[EMAIL PROTECTED]> wrote: >> >>> On Sat, 7 Jun 2008 15:04:34 -0400 >>> "maite lopez cabezas" <[EMAIL PROTECTED]> wrote: >>> Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a Van der Waals radius for 128 atoms 3840 out of 6400 atoms were classified as hydrophobic I saw that the **Van der Waals radius for phophorous atoms doesn't appear in vdwraddi.dat. When I modified it and add the **Van der Waals radius* for this atom and then it works well. But, where were taken the *Van der Waals radius* for Gromacs? Somebody knows the phophorous radius for gromacs? >>> If I am not mistaken the radius used by g_sas are actually defined within >>> the code and it does not use the ones given in cdwradii.dat. >>> >>> have a look a the code you'll find them easily. >>> >> I just had a look at the code. What I said is valid for the gmx-3.1.4. >> In gmx-3.3.3 you have: >> /* Get a Van der Waals radius for each atom */ >> ndefault = 0; >> for(i=0; (i>if (!query_atomprop(atomprop,epropVDW, >>*(top->atoms.resname[top->atoms.atom[i].resnr]), >>*(top->atoms.atomname[i]),&radius[i])) >> ndefault++; >>/* radius[i] = calc_radius(*(top->atoms.atomname[i])); */ >>radius[i] += solsize; >> } >> >> where you can see that the line I was referring to is commented and the >> lines above it have been introduced to get the radius from the topology >> (I think). >> > > No, this does mean that it comes from vdwradii.dat. If there are missing > atoms you can just add them to the file. The only issue is that there are > different sets of radii in use. Which one to use depends on the application. > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [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 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] analysis of different groups with g_energy
Peyman Yamin wrote: On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: Well, ofcourse I did! otherwise I wouldn't expect any program to know them by itself! the problem is that I say: Well, there's a lesson here. You should spell out all relevant data - like your usage of energy groups in your run input file and your full observations of g_energy the first time. We don't read minds here, and Justin's assumption of your probable failure to plan for your own analysis seems to be borne out by the way most new people approach MD simulations :-) # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o tot_ener and I get: Opened ../ener.edr as single precision energy file Select the terms you want from the following list - Angle Proper-Dih. Improper-Dih. LJ-14 Coulomb-14 LJ-(SR) Coulomb-(SR)Coulomb-(LR) RF-excl.Potential Kinetic-En. Total-Energy Temperature Pressure-(bar) Box-X Box-Y Box-Z Volume Density-(SI)pV Vir-XX Vir-XY Vir-XZ Vir-YX Vir-YY Vir-YZ Vir-ZX Vir-ZY Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) Pres-ZY-(bar) Pres-ZZ-(bar) #Surf*SurfTen Pcoupl-Mu-XX Pcoupl-Mu-YYPcoupl-Mu-ZZMu-XMu-Y Mu-ZCoul-SR:OCT-OCT LJ-SR:OCT-OCT Coul-LR:OCT-OCT Coul-14:OCT-OCT LJ-14:OCT-OCT Coul-SR:OCT-TX1 LJ-SR:OCT-TX1 Coul-LR:OCT-TX1 Coul-14:OCT-TX1 LJ-14:OCT-TX1 Coul-SR:TX1-TX1 LJ-SR:TX1-TX1 Coul-LR:TX1-TX1 Coul-14:TX1-TX1 LJ-14:TX1-TX1 T-OCT T-TX1 Lamb-OCTLamb-TX1 without any notification for choosing a group. Actually, that's all the notification you get. You can type a newline-delimited list of the energy terms you'd like, and follow it with a blank line and g_energy will produce your output. You may also like to consult http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive Note, however, that "total energy of group X" is not available. That's because it isn't calculated, and in the vast majority of cases it wouldn't mean anything anyway. You can see a breakdown of the nonbonded interactions there, however. On the other hand, for instance when I say: # g_gyrate -f out.xtc -s ../25ns.tpr I get, in a beautiful way: Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) Opening library file /apps/GMX/331-intel64-intelmpi-wc/share/gromacs/top/aminoacids.dat Group 0 ( System) has 24476 elements Group 1 ( TX1) has46 elements Group 2 ( OCT) has 24430 elements Select a group: Now I don't know why I don't get the same behaviour with g_energy, if at all I should expect such a thing! It's inconsistent, but probably reflects that a different person wrote the two programs. 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] TEE-REX installation error
TJ Piggot wrote: Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF .deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o gmx_parallel_3dfft.o if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF ".deps/qm_gaussian.Tpo" -c -o qm_gaussian.lo qm_gaussian.c; \ then mv -f ".deps/qm_gaussian.Tpo" ".deps/qm_gaussian.Plo"; else rm -f ".deps/qm_gaussian.Tpo"; exit 1; fi if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF ".deps/gmx_fft_fftw3.Tpo" -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \ then mv -f ".deps/gmx_fft_fftw3.Tpo" ".deps/gmx_fft_fftw3.Plo"; else rm -f ".deps/gmx_fft_fftw3.Tpo"; exit 1; fi cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c teerex.c -o teerex.o teerex.c: In function `init_TEEREX': teerex.c:167: warning: implicit declaration of function `MPI_Gather' teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function) teerex.c:167: error: (Each undeclared identifier is reported only once teerex.c:167: error: for each function it appears in.) teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this function) teerex.c:244: warning: implicit declaration of function `MPI_Barrier' These are occurring because teerex.c is expecting to be part of an MPI installation of GROMACS, and yours isn't. Thus either the installation documentation of TEE-REX, or your following of it, is suspect :-) I know nothing about TEE-REX, but your first move after checking their documentation again should be a "make distclean" and then to reconfigure GROMACS with the --enable-mpi flag. 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] extract conformations !!
Anamika Awasthi wrote: Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? That won't be necessary, but there's no particular guarantee that all of your files are in sync, because of the system's I/O buffering. I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000 Please tell me the solution of my this problem http://wiki.gromacs.org/index.php/Doing_Restarts and http://wiki.gromacs.org/index.php/Using_Trajectory_Information have information useful to you, however your answers really are there in the man page of trjconv. However, unless you happen to have exactly one .trr, .pdb and .tpr file in your working directory, your shell globs will not work. Only a handful of tools in GROMACS permit such multiple I/O and trjconv is not one of them. You can tell by the suffix "Input, Mult." on the man page... viz "FILES -f traj.xtc Input, Mult. Generic trajectory: xtc trr trj gro g96 pdb" Next, as the header of each man page indicates, only the flags that label the inputs get hyphens, not both the flags and their input data. This allows the code to distinguish flags from inputs to flags. 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] TEE-REX installation error
Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF .deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o gmx_parallel_3dfft.o if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF ".deps/qm_gaussian.Tpo" -c -o qm_gaussian.lo qm_gaussian.c; \ then mv -f ".deps/qm_gaussian.Tpo" ".deps/qm_gaussian.Plo"; else rm -f ".deps/qm_gaussian.Tpo"; exit 1; fi if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF ".deps/gmx_fft_fftw3.Tpo" -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \ then mv -f ".deps/gmx_fft_fftw3.Tpo" ".deps/gmx_fft_fftw3.Plo"; else rm -f ".deps/gmx_fft_fftw3.Tpo"; exit 1; fi cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c teerex.c -o teerex.o teerex.c: In function `init_TEEREX': teerex.c:167: warning: implicit declaration of function `MPI_Gather' teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function) teerex.c:167: error: (Each undeclared identifier is reported only once teerex.c:167: error: for each function it appears in.) teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this function) teerex.c:244: warning: implicit declaration of function `MPI_Barrier' make[3]: *** [teerex.lo] Error 1 make[3]: *** Waiting for unfinished jobs cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF .deps/qm_gaussian.Tpo -c qm_gaussian.c -o qm_gaussian.o cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF .deps/gmx_fft_fftw3.Tpo -c gmx_fft_fftw3.c -o gmx_fft_fftw3.o make[3]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src' make: *** [all-recursive] Error 1 I am using the gcc 3.4.6 compiler on a CentOS 4 linux box and also gromacs 3.3.1 without the TEE-REX patch installs fine. Thanks for any advice you can give me to fix this problem. Tom Piggot -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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] analysis of different groups with g_energy
On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: Well, ofcourse I did! otherwise I wouldn't expect any program to know them by itself! the problem is that I say: # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o tot_ener and I get: Opened ../ener.edr as single precision energy file Select the terms you want from the following list - Angle Proper-Dih. Improper-Dih. LJ-14 Coulomb-14 LJ-(SR) Coulomb-(SR)Coulomb-(LR) RF-excl.Potential Kinetic-En. Total-Energy Temperature Pressure-(bar) Box-X Box-Y Box-Z Volume Density-(SI)pV Vir-XX Vir-XY Vir-XZ Vir-YX Vir-YY Vir-YZ Vir-ZX Vir-ZY Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) Pres-YX-(bar) Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) Pres-ZY-(bar) Pres-ZZ-(bar) #Surf*SurfTen Pcoupl-Mu-XX Pcoupl-Mu-YYPcoupl-Mu-ZZMu-XMu-Y Mu-ZCoul-SR:OCT-OCT LJ-SR:OCT-OCT Coul-LR:OCT-OCT Coul-14:OCT-OCT LJ-14:OCT-OCT Coul-SR:OCT-TX1 LJ-SR:OCT-TX1 Coul-LR:OCT-TX1 Coul-14:OCT-TX1 LJ-14:OCT-TX1 Coul-SR:TX1-TX1 LJ-SR:TX1-TX1 Coul-LR:TX1-TX1 Coul-14:TX1-TX1 LJ-14:TX1-TX1 T-OCT T-TX1 Lamb-OCTLamb-TX1 without any notification for choosing a group. On the other hand, for instance when I say: # g_gyrate -f out.xtc -s ../25ns.tpr I get, in a beautiful way: Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) Reading file ../25ns.tpr, VERSION 3.3.1 (single precision) Opening library file /apps/GMX/331-intel64-intelmpi-wc/share/gromacs/top/aminoacids.dat Group 0 ( System) has 24476 elements Group 1 ( TX1) has46 elements Group 2 ( OCT) has 24430 elements Select a group: Now I don't know why I don't get the same behaviour with g_energy, if at all I should expect such a thing! regards, Peyman > Choose appropriate energygrps in your .mdp file. > > -Justin > > Peyman Yamin wrote: > > Dear Gromacs users, > > > > I'm simulating dilute solutions of different surfactants in different > > media. All I want to analyse afterwards, though, is the single surfactant > > molecule properties! > > > > Is there any way to extract energy data from the original .edr file with > > respect to a single group, in the same way as one can extract structures > > from an .xdr with trjconvm? > > Is there any way to use g_energy to different groups? as I see I can only > > have some of the properties in a group-specified way - like T! I'm not > > asked in which group i'm interested and neither I can specify it at > > command-line, that I want, say total-energy of group G! > > > > Thanks in advance, > > > > Best regards > > Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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] analysis of different groups with g_energy
Choose appropriate energygrps in your .mdp file. -Justin Peyman Yamin wrote: Dear Gromacs users, I'm simulating dilute solutions of different surfactants in different media. All I want to analyse afterwards, though, is the single surfactant molecule properties! Is there any way to extract energy data from the original .edr file with respect to a single group, in the same way as one can extract structures from an .xdr with trjconvm? Is there any way to use g_energy to different groups? as I see I can only have some of the properties in a group-specified way - like T! I'm not asked in which group i'm interested and neither I can specify it at command-line, that I want, say total-energy of group G! Thanks in advance, Best regards 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
[gmx-users] analysis of different groups with g_energy
Dear Gromacs users, I'm simulating dilute solutions of different surfactants in different media. All I want to analyse afterwards, though, is the single surfactant molecule properties! Is there any way to extract energy data from the original .edr file with respect to a single group, in the same way as one can extract structures from an .xdr with trjconvm? Is there any way to use g_energy to different groups? as I see I can only have some of the properties in a group-specified way - like T! I'm not asked in which group i'm interested and neither I can specify it at command-line, that I want, say total-energy of group G! Thanks in advance, Best regards Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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: Re: [gmx-users] Re:Time evolution of lipidbilayer
Thanks for your prompt reply, Yes I will do further analysis a)thickness of bilayer b) g_order of popc by using 5ns trjectory file. Thank you On Mon, 09 Jun 2008 Justin A.Lemkul wrote : >trjcat, then do your analysis. > >-Justin > >minnale wrote: >>Content-type: multipart/alternative; >> boundary="Next_1213018572---0-202.137.237.238-31592" >> >> This is a multipart mime message >> >> >>--Next_1213018572---0-202.137.237.238-31592 >>Content-type: text/plain; >> charset=iso-8859-1 >>Content-Transfer-Encoding: quoted-printable >>Content-Disposition: inline >> >>=0AThanks for your reply=0ACould you give me a clue about how can I make co= >>ntinuous plot with concatenation of trajectories? if you tell any command t= >>hat will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:= >>=0A>=0A> =0A>> Hi all,=0A>> This may be a trivial question=0A>> I wan= >>t to calculate "time evolution of area per lipid"=0A>> The steps I have don= >>e are=0A>> 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_ene= >>rgy =0A>> command.=0A>> 2. I have written code for calculating area per lip= >>id in way that boxX =0A>> multiply with boxY divided by 64=0A>> 3. I have g= >>ot the plot in this way=0A>> **0 to 1000ps started the value 0.609= >>678 nm^2/N ended with =0A>> 0.642679(shows high peak)=0A>> **then 1000 = >>to 4000ps shows silght variation with 0.64 value( =0A>> nearly straight li= >>ne)=0A>> **at 4000ps the value increased to 0.653465 ( high peak) from = >>=0A>> there it reduced again to 0.647856 =0A>>=0A>> I want to ask you that = >>the way values are got correct? and suggest me =0A>> some articles regardin= >>g area per lipid=0A>>=0A=0A>Your calculations seem reasonable, and you coul= >>d also concatenate your =0A>trajectories to get one continuous plot to make= >> things simpler. The =0A>value seems about right for POPC, but it's been a= >> while since I >checked =0A>the exact number.=0A=0A>As far as literature go= >>es, a simple Google search will turn up lots of =0A>useful results. And if= >> you're using the lipid parameters from =0A>Tieleman's site, his publicatio= >>n list is a good place to start.=0A=0A->Justin=0A=0A> >Thanks for your aprr= >>eciation.=0A> >>--Next_1213018572---0-202.137.237.238-31592 >>Content-type: text/html; >> charset=iso-8859-1 >>Content-Transfer-Encoding: quoted-printable >>Content-Disposition: inline >> >>=0A=0AThanks for your reply=0ACould you give me a clue about how= >> can I make continuous plot with concatenation of trajectories? if you tell= >> any command that will be really helpful to me=0A=0AThanking you.>R>=0A =0Aminnale wrote:=0A>=0A> =0A>&g= >>t; Hi all,=0A>> This may be a trivial question=0A>&g= >>t; I want to calculate "time evolution of area per lipid= >>"=0A>> The steps I have done are=0A>> 1. Extracted= >> BoxX and BoxY values of 5ns_popc.edr by using g_energy =0A>> com= >>mand.=0A>> 2. I have written code for calculating area per lipid = >>in way that boxX =0A>> multiply with boxY divided by 64=0A>= >>;> 3. I have got the plot in this way=0A>> **0 t= >>o 1000ps started the value 0.609678 nm^2/N ended with =0A>> = >>0.642679(shows high peak)=0A>> **then 1000 to 4000p= >>s shows silght variation with 0.64 value( =0A>> nearly stra= >>ight line)=0A>> **at 4000ps the value increased to = >>0.653465 ( high peak) from =0A>> there it reduced again to 0.6478= >>56 =0A>>=0A>> I want to ask you that the way values are= >> got correct? and suggest me =0A>> some articles regarding area p= >>er lipid=0A>>=0A=0A>Your calculations seem reasonable,= >> and you could also concatenate your =0A>trajectories to get one con= >>tinuous plot to make things simpler. The =0A>value seems about= >> right for POPC, but it's been a while since I >checked =0A>the e= >>xact number.=0A=0A>As far as literature goes, a simple Google se= >>arch will turn up lots of =0A>useful results. And if you're us= >>ing the lipid parameters from =0A>Tieleman's site, his publication l= >>ist is a good place to start.=0A=0A->Justin=0A=0A> &g= >>t;Thanks for your aprreciation.=0A>=0A=0A=0A>r=3D0 Width=3D644 Height=3D57 cellspacing=3D0 cellpadding=3D0 style=3D'font= >>-family:Verdana;font-size:11px;line-height:15px;'>>://imadworks.rediff.com/cgi-bin/AdWorks/adimage.cgi/2129697_2122129/creativ= >>e_2129852.gif' alt=3D'Amity' border=3D0> >>--Next_1213018572---0-202.137.237.238-31592-- >> >>___ >>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 >
Re: [gmx-users] Re:Time evolution of lipidbilayer
trjcat, then do your analysis. -Justin minnale wrote: Content-type: multipart/alternative; boundary="Next_1213018572---0-202.137.237.238-31592" This is a multipart mime message --Next_1213018572---0-202.137.237.238-31592 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =0AThanks for your reply=0ACould you give me a clue about how can I make co= ntinuous plot with concatenation of trajectories? if you tell any command t= hat will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:= =0A>=0A> =0A>> Hi all,=0A>> This may be a trivial question=0A>> I wan= t to calculate "time evolution of area per lipid"=0A>> The steps I have don= e are=0A>> 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_ene= rgy =0A>> command.=0A>> 2. I have written code for calculating area per lip= id in way that boxX =0A>> multiply with boxY divided by 64=0A>> 3. I have g= ot the plot in this way=0A>> **0 to 1000ps started the value 0.609= 678 nm^2/N ended with =0A>> 0.642679(shows high peak)=0A>> **then 1000 = to 4000ps shows silght variation with 0.64 value( =0A>> nearly straight li= ne)=0A>> **at 4000ps the value increased to 0.653465 ( high peak) from = =0A>> there it reduced again to 0.647856 =0A>>=0A>> I want to ask you that = the way values are got correct? and suggest me =0A>> some articles regardin= g area per lipid=0A>>=0A=0A>Your calculations seem reasonable, and you coul= d also concatenate your =0A>trajectories to get one continuous plot to make= things simpler. The =0A>value seems about right for POPC, but it's been a= while since I >checked =0A>the exact number.=0A=0A>As far as literature go= es, a simple Google search will turn up lots of =0A>useful results. And if= you're using the lipid parameters from =0A>Tieleman's site, his publicatio= n list is a good place to start.=0A=0A->Justin=0A=0A> >Thanks for your aprr= eciation.=0A> --Next_1213018572---0-202.137.237.238-31592 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =0A=0AThanks for your reply=0ACould you give me a clue about how= can I make continuous plot with concatenation of trajectories? if you tell= any command that will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:=0A>=0A> =0A>&g= t; Hi all,=0A>> This may be a trivial question=0A>&g= t; I want to calculate "time evolution of area per lipid= "=0A>> The steps I have done are=0A>> 1. Extracted= BoxX and BoxY values of 5ns_popc.edr by using g_energy =0A>> com= mand.=0A>> 2. I have written code for calculating area per lipid = in way that boxX =0A>> multiply with boxY divided by 64=0A>= ;> 3. I have got the plot in this way=0A>> **0 t= o 1000ps started the value 0.609678 nm^2/N ended with =0A>> = 0.642679(shows high peak)=0A>> **then 1000 to 4000p= s shows silght variation with 0.64 value( =0A>> nearly stra= ight line)=0A>> **at 4000ps the value increased to = 0.653465 ( high peak) from =0A>> there it reduced again to 0.6478= 56 =0A>>=0A>> I want to ask you that the way values are= got correct? and suggest me =0A>> some articles regarding area p= er lipid=0A>>=0A=0A>Your calculations seem reasonable,= and you could also concatenate your =0A>trajectories to get one con= tinuous plot to make things simpler. The =0A>value seems about= right for POPC, but it's been a while since I >checked =0A>the e= xact number.=0A=0A>As far as literature goes, a simple Google se= arch will turn up lots of =0A>useful results. And if you're us= ing the lipid parameters from =0A>Tieleman's site, his publication l= ist is a good place to start.=0A=0A->Justin=0A=0A> &g= t;Thanks for your aprreciation.=0A>=0A=0A=0A --Next_1213018572---0-202.137.237.238-31592-- ___ 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
[gmx-users] Re:Time evolution of lipidbilayer
Content-type: multipart/alternative; boundary="Next_1213018572---0-202.137.237.238-31592" This is a multipart mime message --Next_1213018572---0-202.137.237.238-31592 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =0AThanks for your reply=0ACould you give me a clue about how can I make co= ntinuous plot with concatenation of trajectories? if you tell any command t= hat will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:= =0A>=0A> =0A>> Hi all,=0A>> This may be a trivial question=0A>> I wan= t to calculate "time evolution of area per lipid"=0A>> The steps I have don= e are=0A>> 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_ene= rgy =0A>> command.=0A>> 2. I have written code for calculating area per lip= id in way that boxX =0A>> multiply with boxY divided by 64=0A>> 3. I have g= ot the plot in this way=0A>> **0 to 1000ps started the value 0.609= 678 nm^2/N ended with =0A>> 0.642679(shows high peak)=0A>> **then 1000 = to 4000ps shows silght variation with 0.64 value( =0A>> nearly straight li= ne)=0A>> **at 4000ps the value increased to 0.653465 ( high peak) from = =0A>> there it reduced again to 0.647856 =0A>>=0A>> I want to ask you that = the way values are got correct? and suggest me =0A>> some articles regardin= g area per lipid=0A>>=0A=0A>Your calculations seem reasonable, and you coul= d also concatenate your =0A>trajectories to get one continuous plot to make= things simpler. The =0A>value seems about right for POPC, but it's been a= while since I >checked =0A>the exact number.=0A=0A>As far as literature go= es, a simple Google search will turn up lots of =0A>useful results. And if= you're using the lipid parameters from =0A>Tieleman's site, his publicatio= n list is a good place to start.=0A=0A->Justin=0A=0A> >Thanks for your aprr= eciation.=0A> --Next_1213018572---0-202.137.237.238-31592 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =0A=0AThanks for your reply=0ACould you give me a clue about how= can I make continuous plot with concatenation of trajectories? if you tell= any command that will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:=0A>=0A> =0A>&g= t; Hi all,=0A>> This may be a trivial question=0A>&g= t; I want to calculate "time evolution of area per lipid= "=0A>> The steps I have done are=0A>> 1. Extracted= BoxX and BoxY values of 5ns_popc.edr by using g_energy =0A>> com= mand.=0A>> 2. I have written code for calculating area per lipid = in way that boxX =0A>> multiply with boxY divided by 64=0A>= ;> 3. I have got the plot in this way=0A>> **0 t= o 1000ps started the value 0.609678 nm^2/N ended with =0A>> = 0.642679(shows high peak)=0A>> **then 1000 to 4000p= s shows silght variation with 0.64 value( =0A>> nearly stra= ight line)=0A>> **at 4000ps the value increased to = 0.653465 ( high peak) from =0A>> there it reduced again to 0.6478= 56 =0A>>=0A>> I want to ask you that the way values are= got correct? and suggest me =0A>> some articles regarding area p= er lipid=0A>>=0A=0A>Your calculations seem reasonable,= and you could also concatenate your =0A>trajectories to get one con= tinuous plot to make things simpler. The =0A>value seems about= right for POPC, but it's been a while since I >checked =0A>the e= xact number.=0A=0A>As far as literature goes, a simple Google se= arch will turn up lots of =0A>useful results. And if you're us= ing the lipid parameters from =0A>Tieleman's site, his publication l= ist is a good place to start.=0A=0A->Justin=0A=0A> &g= t;Thanks for your aprreciation.=0A>=0A=0A=0A --Next_1213018572---0-202.137.237.238-31592-- ___ 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] extract conformations !!
Hi, On Monday, 9. June 2008 13:34, Anamika Awasthi wrote: > Dear Friends, >I want to extract conformations of each 1 ns from my 10 ns > simulation. >My this job is running for 20 ns, so shall I first stop my job and > then do this? >I tried this command without stopping my job > trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000 try something like: trjconv -f traj.trr -s start.tpr -o conformation.pdb - dt 1000 -sep It will split the file already to pdb file. Read also: http://wiki.gromacs.org/index.php/Average_Structure > >Please tell me the solution of my this problem > > Thanks > Anamika Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] Time evolution of lipidbilayer
minnale wrote: Hi all, This may be a trivial question I want to calculate "time evolution of area per lipid" The steps I have done are 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_energy command. 2. I have written code for calculating area per lipid in way that boxX multiply with boxY divided by 64 3. I have got the plot in this way **0 to 1000ps started the value 0.609678 nm^2/N ended with 0.642679(shows high peak) **then 1000 to 4000ps shows silght variation with 0.64 value( nearly straight line) **at 4000ps the value increased to 0.653465 ( high peak) from there it reduced again to 0.647856 I want to ask you that the way values are got correct? and suggest me some articles regarding area per lipid Your calculations seem reasonable, and you could also concatenate your trajectories to get one continuous plot to make things simpler. The value seems about right for POPC, but it's been a while since I checked the exact number. As far as literature goes, a simple Google search will turn up lots of useful results. And if you're using the lipid parameters from Tieleman's site, his publication list is a good place to start. -Justin Thanks for your aprreciation. Amity ___ 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] extract conformations !!
Anamika Awasthi wrote: Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000 Use trjconv -sep -skip to write frames to .gro or .pdb files. It will be faster than dumping out individual frames manually. -Justin Please tell me the solution of my this problem Thanks Anamika ___ 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
[gmx-users] extract conformations !!
Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000 Please tell me the solution of my this problem Thanks Anamika ___ 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] Time evolution of lipidbilayer
Hi all, This may be a trivial question I want to calculate "time evolution of area per lipid" The steps I have done are 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_energy command. 2. I have written code for calculating area per lipid in way that boxX multiply with boxY divided by 64 3. I have got the plot in this way **0 to 1000ps started the value 0.609678 nm^2/N ended with 0.642679(shows high peak) **then 1000 to 4000ps shows silght variation with 0.64 value( nearly straight line) **at 4000ps the value increased to 0.653465 ( high peak) from there it reduced again to 0.647856 I want to ask you that the way values are got correct? and suggest me some articles regarding area per lipid Thanks for your aprreciation.___ 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
