[gmx-users] Question about NVT
Hello all, I have a quick question regarding an MD simulation I am attempting to run (again, the membrane protein which I had problems with previously). Thanks to the helpful suggestions; my system is now well-minimized! The last step before I would like to take before running full-out MD on my system is to equilibrate my solvent and ions over a short timeframe (100ps). My initial attempts have been unsuccessful; the equilibration proceeds nicely for 960 steps (1.920 ps) before I get a screen full of LINCS warnings. Apparently one of my DPPC molecules is being blown apart. I have placed position restraints on both my protein and my bilayer, in order to allow the solvent and ions (Na+) to move around them. I have attached my equil.mdp file below, in case I am making any obvious mistakes. I am piecing my .mdp file together from several examples and tutorials. My value for nstlog is set very small so I could monitor energies, etc after the first failure...in case anyone was wondering :) Thanks in advance for your kind advice in helping out a newbie. -Justin PS - I'm running Gromacs v3.3 on Mac OSX v10.4.8, in case any of that matters. -- title= MD equilibration of solvent and ions cpp = /usr/bin/cpp include = -I./ define = -DPOSRES -DPOSRES_LIPID integrator = md nsteps = 5 nstlist = 10 nstxout = 1000 nstvout = 1000 nstlog = 10 nstenergy= 1000 nstxtcout= 1000 dt = 0.002 ns_type = simple coulombtype = cut-off rlist= 0.9 rvdw = 0.9 rcoulomb = 0.9 fourierspacing = 0.12 ; Temperature coupling is on in four groups tcoupl = berendsen tc_grps = Protein DPPC SOL NA+ tau_t= 0.1 0.1 0.1 0.1 ref_t= 323 323 323 323 ; Pressure coupling is not on Pcoupl = no ref_p= 1.0 gen_vel = no gen_temp = 323 constraints = all-bonds constraint_algorithm = lincs optimize_fft = yes DispCorr = EnerPres pbc = full - Justin A. Lemkul Department of Biochemistry Virginia Tech ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Segmentaion fault error- installing gromacs-3.3.1 on MacOSX
Hi gmx-users,
I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
After installation (either building the package myself as instructed,
or using a binary form GROMACS web site) I could not run any program
with just typing the name on the xterm!
for example, issuing "pdb2gmx" command line gives an error message
"segmentation fault". However, typing the whole path name
"$GMXBIN/pdb2gmx or any other modules " works fine.
The variables for GROMACS are configured after the installation. My
.cshrc sources from the GMXRC.csh and the variables are defined; the
PATH includes the $GMXBIN also.
For the moment, I'm using alias to define the whole path for GROMACS
programs to run; though, this a bit annoying.
I posted this problem in CCL and M.L. Dodson, replied with some
explanation for this weird problem:
" Ahh... Think I have it. Looking at the source code on my BSD Unix
box, I see in src/gmxlib/copyrite.c the following:
void CopyRight(FILE *out,char *szProgram)
{
/* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
* name of a file. Otherwise, we won't be able to find the library dir.
*/
#define NCR (int)asize(CopyrightText)
#define NGPL (int)asize(GPLText)
char buf[256],tmpstr[1024];
char *ptr;
int i;
set_program_name(szProgram);
.
.
.
So I was right, it does use argv[0] for something: finding its
library directory."
I wonder if there is a quick fix for this in the code, so I can
run the programs by just typing the name without need for the whole path!
A question here: if Dodson is right, why the programer wrote the
code this way! is there any advantage?
P.S. I have no previous experience with GROMACS
thanks,
Ibrahim
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[gmx-users] opls parameters
Hi All, I am trying to build the itp file for a molecule. I would like to use the opls force field. The ffoplsaa.atp contains the atom types as opls_xxx. But the ffoplsbon.itp which contains the bond-angle-dihedral parameters does not use the opls_xxx convention. Is there a way to identify the bond/angle/torsion parameters of a set of opls_xxx atoms? Thanks very much! Dam --- Komath Damodaran Scientist, Computational Chemistry Telik, Inc. 3165 Porter Drive Palo Alto, CA 94304 Tel: (650) 845-7838, Fax: 650-845-7800 === This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Surface Tension of a lipid bilayer
Hello, I have a question about calculating the surface tension for the water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr file and g_energy to calculate the surface tension. I believe that the surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L. I was wondering though, is the pressure tensor and hence surface tension calculated over the entire simulation box? I would assume so, since I did not specify any molecules. To find the water-lipid surface tension, would I not need to sum over only the molecules at the surface? Would this be do-able in Gromacs? Would I have to write something separate to do this? In my coordinate file, I have DPPC atoms, solvent atoms, and other atoms (those that make up the head group ie O,N etc.). Could I just make an index group that is not DPPC and not Solvent, and sum over those atoms? Thanks, Mike Tomasini ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editing HDB file ???
You may study it by comparing the structure of h-added peptide or single amino acid. On 12/2/2006 12:31 AM, Karthikeyan Pasupathy wrote: How do i edit .hdb file ? what is the format .? i could not find it in the gromacs manual. thanks, Karthikeyan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editing HDB file ???
Karthikeyan, Chapter 5.5.2 Cheers, Tsjerk On 12/1/06, Karthikeyan Pasupathy <[EMAIL PROTECTED]> wrote: How do i edit .hdb file ? what is the format .? i could not find it in the gromacs manual. thanks, Karthikeyan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editing HDB file ???
How do i edit .hdb file ? what is the format .? i could not find it in the gromacs manual. thanks, Karthikeyan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] I need 256 lipids ...
Stéphane Téletchéa wrote: David van der Spoel a écrit : Stéphane Téletchéa wrote: editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc But unfortunately, some lipids are not imaged (at least 18, 25 and 53). I tried using trjconv but it needs a topol.tpr that i don't have :-( Any hint ? Stéphane It requires some manual work, but with editconf you can translate a subset of atoms, so you have to find out which atoms they are, and then write an index file, and then translate them by one box. It works now ! Just for the record, here are the steps i did to obtain a usable file: 1 - editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc At this step, 4 lipids are not correctly imaged (18, 23, 25 and 53). The problem is the same for all of them, one palmitoyl tail is not imaged to its counterpart. I presume this comes form the way the algorithm tries to guess the tail to image. 3 DPPC (18,25 and 53) need to get their tail back via a -x translation, DPPC 23 needs a -y translation. To perform this: 2 - editconf -f dppc64_pbc1.pdb -o dppc64_pbcx.pdb -n grouptomove_x.ndx -translate -4.7245 0 0 3 - editconf -f dppc64_pbc1.pdb -o dppc64_pbcy.pdb -n grouptomove_y.ndx -translate 0 -4.2319 0 4 - edit manually the files to correct the coordinates. If there's a need, i can do a better explanation and provide files on my website, feel free to ask. Thanks for the help, Stéphane maybe you can forward your "corrected" files to Peter Tieleman, since this is where people look for these files. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] indexing atoms *Altering code
toma0052 wrote: Hi, Thank you for the response. Being that Fortran is much more my language of choice than C, I was wondering if someone could point me in the right direction as far as modifying the C code to do what I want. It is my understanding that an mdrun begins by making a neighbor list, computing the forces, globally summing the forces, and then updating the positions and velocities. So I am assuming that, just after globally summing the forces, I can run an if statement over all of the solvent molecules testing whether their z-coordinate is within certain bounds, and if so, simply add Fsum = Fsum + Fext. My question is, where do I do this? Do I have to do it in multiple files? Where are those files stored in Gromacs? Is it the mdrun.h and force.h files that I need to modify? Sorry if this should be obvious, but again, my C skills are not the best. Go to src/mdlib/sim_util.c Look at the code in function efield (electric field). If your external force is just a function of the Z coord you can make a similar function that you call straight after the electric field function is called. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Official charmm support
I appreciate your suggestion! It shouldn't be hard; a quick look tells me there are only some unconventional "tags" (compared to the standard charmm ff defs) in this ff definition the porting script has to cope with. I'll address the matter as soon as we're done with the port supporting cmap. It probably won't be tested though... Cheers, Par Bjelkmar > I would like to suggest that you include the > carbohydrate force field of J Brady (CSFF). Here are > some references and download sites > > Journal of computational chemistry 2002, vol. 23, > no13, pp. 1236-1243 > http://people.cs.uct.ac.za/~mkuttel/downloads.html > > Thanks > > Gil Claudio > > > > Dear gromacs users, > > > > I'm a new PhD student in Erik Lindahl's group and we > > are currently > > working on an "official" implementation of the > > charmm ff in gromacs > > which also supports CMAP. There's still some more > > work needed on the > > CMAP part but we intend to have a (thoroughly) > > tested version of the > > protein lipid charmm force field completed New > > Yearish. The problem with > > the multiple entries (see thread "CHARMM force field > > implementation in > > Gromacs" in gmx-users) of certain (proper) dihedrals > > where at least one > > has a multiplicity > 5 is also supported by adding a > > new dihedral > > type. > > > > The testing of other system types is something we > > would like to > > outsource on the gromacs users interested in them > > since we don't > > normally study other systems than protein-lipid ones > > in the group. If > > you have a specific system you would like to test in > > our new gromacs > > version and cannot wait until it's released, please > > contact me and we > > could arrange something. > > > > Yours, > > Pär > > -- > > > * > > Pär BjelkmarStockholm Center for > > Biomembrane Research > > Tel: +46-8-16 2746 Dep of Biochemistry and > > Biophysics > > Fax: +46-8-15 3679 Stockholm University > > [EMAIL PROTECTED] 10691 Stockholm, Sweden > > * > > > > > Want to start your own business? > Learn how on Yahoo! Small Business. > http://smallbusiness.yahoo.com/r-index > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- * Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] strange NTP trajectory
Do you have anything like -DPOSRE... for define in your mdp file? Yang Ye On 12/1/2006 8:18 PM, Qiao Baofu wrote: Hi all, I run NTV firstly for 100ps, then change to NTP for 1ns. The mdrun finished with the common informations. But when I use vmd (or ngmx) to look at the trajectory, I found that during the NTP stage, starting from 100ps, all the molecules don't move except only one molecules. The output file .gro of NTP seems ok. Who knows the reason? Sincerely yours, Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] strange NTP trajectory
Hi all, I run NTV firstly for 100ps, then change to NTP for 1ns. The mdrun finished with the common informations. But when I use vmd (or ngmx) to look at the trajectory, I found that during the NTP stage, starting from 100ps, all the molecules don't move except only one molecules. The output file .gro of NTP seems ok. Who knows the reason? Sincerely yours, Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About g_cluster
Hi, Can anybody give some reference about a good explanation on how to use g_cluster in order to analyze a set of simulations on complexes differing one each other in their starting point conformation? Thanks in adavance, César.- --- Cesar Araujo, Lic. of Chemistry Research Center for Molecular Endocrinology P.O. Box 5000, FIN-90014 University of Oulu Finland phone: +358 8 3155632 e-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] I got error in gromacs-3.2.1 installation time
ankit ashwinbhai patel wrote: Hello Friends, I am new to gromacs. I configure the gromacs than it did not give me error but when i run make command that it gave me following error. mpicc -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/usr/include/libxml2 -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o dum_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o -L/home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/fftw/lib ../mdlib/.libs/libmd_mpi.a -L/usr/X11R6/lib ../gmxlib/.libs/libgmx_mpi.a -lnsl /home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/fftw/lib/librfftw_mpi.a /home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/fftw/lib/libfftw_mpi.a /home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/fftw/lib/librfftw.a /home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/fftw/lib/libfftw.a -lX11 -lxml2 -lz -lpthread -lm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/gromacs-3.2.1/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/gromacs-3.2.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/sgeadmin/gromacs/gromacs-test/gromacs-3.2/gromacs-3.2.1/src' make: *** [all-recursive] Error 1 I think it gave me error for mpicc command but it's there in the path. So please help me in this problem. Thanks in advance You'll need to tell us some useful information, like the architecture, the OS, the compiler version, the MPI distribution, your configure command line (it's in config.log). Oh, and start with the latest version of gromacs, not 3.2.1, especially if I psychically guess that this machine is a Mac. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
