RE: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel]
> Date: Tue, 22 Jan 2008 20:15:03 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run > across nodes in parallel] > > Hi Erik, > > I have made a test with today's CVS version and I also run into the > problem you described. It happens as soon as one uses more than one node > and at the same time more than one process per node. > > The problem seems to be in gmx_sumd where in the two-step summation in a > call to MPI_Allreduce the variable cr->nc.comm_inter happens to be a > NULL pointer, which should clearly not be. > > The inter-node communicator is freed in gmx_setup_nodecomm (network.c, > line 393) if an intra-node communicator is present - I do not understand > why the communicator is freed here. > > Maybe Berk can help us on that? If I comment out the MPI_Comm_free the > code runs happily - haven't checked the results, though. > > Carsten Ah, there is a "typo" in the conditional, it should be rank_intra iso comm_intra. I have committed the fix. Thanks, Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] potential tables not working
Hello all, I am trying to learn to use tabulated potential in GROAMCS for defining my own potential. For learning purposes I have created a pdb of silicon atoms of 28 atoms. I want to create two groups each of which will interact in a different way . The gro file is GRowing Old MAkes el Chrono Sweat 28 1SI SI1 0.229 0.250 0.500 2SI SI2 0.589 0.250 0.500 3SI SI3 0.948 0.250 0.500 4SI SI4 1.297 0.250 0.500 5SI SI5 1.666 0.250 0.500 6SI SI6 2.025 0.250 0.500 7SI SI7 2.385 0.250 0.500 8SI SI8 2.744 0.250 0.500 9SI SI9 3.103 0.250 0.500 10SI SI 10 0.050 0.561 0.500 11SI SI 11 0.409 0.561 0.500 12SI SI 12 0.768 0.561 0.500 13SI SI 13 1.127 0.561 0.500 14SI SI 14 1.487 0.561 0.500 15SI SI 15 1.846 0.561 0.500 16SI SI 16 2.205 0.561 0.500 17SI SI 17 2.574 0.561 0.500 18SI SI 18 3.283 0.561 0.720 19SI SI 19 0.229 0.872 0.720 20SI SI 20 0.589 0.872 0.720 21SI SI 21 0.948 0.872 0.720 22SI SI 22 1.297 0.872 0.720 23SI SI 23 1.666 0.872 0.720 24SI SI 24 2.025 0.872 0.720 25SI SI 25 2.385 0.872 0.720 26SI SI 26 2.744 0.872 0.720 27SI SI 27 3.103 0.872 0.720 28SI SI 28 0.050 1.183 0.720 3.23280 2.93330 2.21980 Now I make a index file which is as shown [ s1 ] 123456789 10 11 12 13 14 [ s2 ] 15 16 17 18 19 20 21 22 23 24 25 26 27 28 The mdp file is as shown title= md cpp = cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 1 nstcomm = 1 nstxout = 10 nstvout = 10 nstfout = 10 nstxtcout= 0 nstcheckpoint= 20 table-extension = 0 vdwtype = user xtc_grps = s1 s2 energygrps = s1 s2 energygrp_table = s1 s1 s2 s2 s1 s2 nstlist = 10 ns_type = simple rlist= 0.5 coulombtype = user rcoulomb = 0.5 rvdw = 0.5 tcoupl = Berendsen tc-grps = s1 s2 tau_t= 0.1 0.1 ref_t= 300 300 acc-grps = s1 accelerate = 0.004108 0.00 0.00 gen-vel = yes nstenergy= 10 constraints = none Then i proceed on to the making the tpr file and making the run. I give the following command for run: mdrun -nice 0 -v -s cgi.tpr -o cgi1.trr -c chi1.gro -e cgi1.edr -g cgi1.log -table table.xvg -tablep table_s1_s1.xvg -tablep table_s1_s2.xvg -tablep table_s2_s2.xvg The simulation runs okay but the log file is full of infinite numbers. It says Large VCM(group rest): 13422573811400704.0, 97768580317184.0, -12705115630731264.0, ekin-cm: 1.34288e+35 Step Time Lambda 1000.020000.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 0.0e+000.0e+000.0e+00nannan Temperature Pressure (bar) nannan Step Time Lambda 2000.040000.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 0.0e+000.0e+000.0e+00nannan Temperature Pressure (bar) nannan Can somebody tell me why the mdrun is not taking the tables as expected. I have separate tables for table.xvg , table_s1_s1.xvg , table_s1_s2.xvg , table_s2_s2.xvg in the folder where my other files are and "s1" and "s2" are name of the groups. Thanks in advance, Avinash Kumar ___ 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 chance to concatenate (fast) more than 1000 energy files....(Solved!!!)
Thanks to Enry, Justin and Mark. As you told me the best way to do the concatenation is : eneconv *.edr -o outfile.edr. -- Sergio Garay Facultad de Bioquimica y Cs. Biológicas Santa Fe (3000) Argentina Casilla de Correo ___ 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: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel]
Hi Carsten and Berk, Your fixes did the trick. Man, there is some great scaling on the CVS version now! Thanks a lot for the help! / Erik ons 2008-01-23 klockan 09:20 +0100 skrev Berk Hess: > > > > > Date: Tue, 22 Jan 2008 20:15:03 +0100 > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run > > across nodes in parallel] > > > > Hi Erik, > > > > I have made a test with today's CVS version and I also run into the > > problem you described. It happens as soon as one uses more than one node > > and at the same time more than one process per node. > > > > The problem seems to be in gmx_sumd where in the two-step summation in a > > call to MPI_Allreduce the variable cr->nc.comm_inter happens to be a > > NULL pointer, which should clearly not be. > > > > The inter-node communicator is freed in gmx_setup_nodecomm (network.c, > > line 393) if an intra-node communicator is present - I do not understand > > why the communicator is freed here. > > > > Maybe Berk can help us on that? If I comment out the MPI_Comm_free the > > code runs happily - haven't checked the results, though. > > > > Carsten > > Ah, there is a "typo" in the conditional, it should be rank_intra iso > comm_intra. > I have committed the fix. > > Thanks, > > Berk. > > _ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- Erik Brandt <[EMAIL PROTECTED]> KTH ___ 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 remove H atom from residue in gro file?
Dear All, Just to confirm what Justin said, my MD worked flawlessly with his ffG43a1p files. The only issue was that I had to change my pr.mdp and md.mdp files, following a suggestion I found here: I changed the T coupling groups to "Protein" and "Non-Protein" (I am using the same temperature for the whole system anyway). Many thanks for all your help. Best regards, Nelson On Jan 18, 2008 5:50 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Dear All, > > In working with Nelson on his problem (below), I made some headway into > figuring > out what is going on with the ffG43a1p force field files. I know a few others > have asked questions about it across this list, so I thought I would send this > out to everyone. > > By modifying a few entries in the .hdb file, the problems seem to be > alleviated > (as in, the residues are recognized and pdb2gmx proceeds without any errors). > It seems that perhaps the formatting of the .hdb file has changed since a > previous version of Gromacs, but this change has not been reflected in the > ffG43a1p* files. I made no changes to the parameters or the entries in the > original files, only the formatting. > > If anyone has a need for the complete set of ffG43a1p files, please email me > (off-list), and I will be happy to send them along. If there is a widespread > demand for them, I will upload them to the User Contributions site. Hopefully > they will work :) I have not tested them extensively, but I looked into it > because I was curious. > > -Justin > > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > Nelson, > > > > A long while back, a member of our lab contemplated simulating a > > phosphorylated > > protein, but ran into some issues as well. I tried to help him by editing > > the > > ffG43a1p files, and I seem to remember making some headway. If you'd like, > > you > > can send me your .pdb file (off-list) and I'll test it against my ffG43a1p > > files. If it works, I can send you my modifications. I made no changes to > > the > > force field parameters, only the formatting of the files themselves. > > > > -Justin > > > > Quoting Nelson Cotrim <[EMAIL PROTECTED]>: > > > > > Hi Justin, > > > Thanks for the reply. > > > Yes, I used PRODRG Beta. Thanks for the heads up about the charges. > > > The error I got using ffG43a1 was this: > > > >Fatal error: > > > > wrong format in input file ffG43a1p.hdb on line > > > >2 7 OW > > > which was also described here: > > > http://www.gromacs.org/pipermail/gmx-users/2007-August/028977.html > > > but that did not solve my problem. I removed all the unnecessary > > > entries from the hdb file, keeping only the SEP and P data, and then > > > there was another error in yet another ffG43a1p file (I don't remember > > > which one right now). I removed all ffG43a1p files and rolled back the > > > files changed by ffG43a1p to the original ones from Gromacs 3.3.1 and > > > tried PRODRG. > > > So far, everything is going smoothly - I am running the dynamic even > > > so (it's a small one, takes me just two days of computer time and > > > there are no other MDs to run), to make sure everything goes right - > > > the PO3 keeps its tetrahedrical shape, grompp and mdrun runs > > > smoothly... I just will not be able to use the results because there > > > is this extra hydrogen atom which I do not know how to remove from the > > > .gro and .top files. > > > Nelson > > > ___ > > > 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 > > [EMAIL PROTECTED] | (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 > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > ___ > gmx-users mail
[gmx-users] comm_grps
Dear All, I am a little confused with the application of comm_grps. I have a lipid-peptide system in which I am using the default values i.e. comm_mode: linear nstcomm: 1 comm_grps: whole system Is there something wrong with defining comm_grps = whole system for the lipid-peptide case? Is it necessary to define lipid+peptide and solvent separately? Eagerly waiting for the reply, Priyanka Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ 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] installation problem for MAC OS
Dear all, I have difficulties when I try to install Gromacs 3.3.2 in my MAC OS. Please see the following for details. configuration: $ ./configure CC=icc CXX=icc F77=ifort --prefix=/Users/yunan/usr/local/Gromacs --with-qmmm-cpmd --with-fft=fftw3 CLAGS=-no-multibyte-chars CPP=/usr/bin/cpp System information: uname -m = i386 uname -r = 9.1.0 uname -s = Darwin uname -v = Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 /usr/bin/hostinfo = Mach kernel version: Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 Kernel configured for up to 8 processors. 8 processors are physically available. 8 processors are logically available. Processor type: i486 (Intel 80486) configure:3291: icc -V Intel(R) C Compiler for applications running on IA-32, Version 10.1 Build 20070913 Package ID: m_cc_p_10.1.006 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. Error: icc -funroll-all-loops -I/Users/yunan/usr/local/lib -framework Accelerate -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o compute_io.o ../mdlib/.libs/libmd.a -L/usr/X11/lib ../gmxlib/.libs/libgmx.a -lfftw3f /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib ld: in ../gmxlib/.libs/libgmx.a(nb_kernel204_ia32_sse.o), in section __TEXT,__text reloc 1: bad pc-rel vanilla relocation length The same will happen when I use gcc compiler. Does someone have some ideas about what's going on here and how to figure it out? Thanks a lot. Best regards, Yun-an ___ 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] installation problem for MAC OS
Hello! A quick fix so that you will be able to compile, is to try to run the configure script with the flag --disable-ia32-sse. Hopefully you should get a working installation, but with no sse- support (which might be what you want :-) Cheers /Per 23 jan 2008 kl. 14.24 skrev Yunan Yan: Dear all, I have difficulties when I try to install Gromacs 3.3.2 in my MAC OS. Please see the following for details. configuration: $ ./configure CC=icc CXX=icc F77=ifort --prefix=/Users/yunan/usr/local/Gromacs --with-qmmm-cpmd --with- fft=fftw3 CLAGS=-no-multibyte-chars CPP=/usr/bin/cpp System information: uname -m = i386 uname -r = 9.1.0 uname -s = Darwin uname -v = Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 /usr/bin/hostinfo = Mach kernel version: Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 Kernel configured for up to 8 processors. 8 processors are physically available. 8 processors are logically available. Processor type: i486 (Intel 80486) configure:3291: icc -V Intel(R) C Compiler for applications running on IA-32, Version 10.1 Build 20070913 Package ID: m_cc_p_10.1.006 Copyright (C) 1985-2007 Intel Corporation. All rights reserved. Error: icc -funroll-all-loops -I/Users/yunan/usr/local/lib -framework Accelerate -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o compute_io.o ../mdlib/.libs/libmd.a -L/usr/X11/lib ../gmxlib/.libs/libgmx.a -lfftw3f /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib ld: in ../gmxlib/.libs/libgmx.a(nb_kernel204_ia32_sse.o), in section __TEXT,__text reloc 1: bad pc-rel vanilla relocation length The same will happen when I use gcc compiler. Does someone have some ideas about what's going on here and how to figure it out? Thanks a lot. Best regards, Yun-an ___ 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[2]: [gmx-users] Virtual site and constraints
OK, could I add "dummy mass" that has coordinates and mass such as carbon to keep right moment of inertia? I mean something like this: [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1FMT H 1 0.22 1.008 2 opls_271 1FMT C 1 0.58 0.000 3 opls_272 1FMT O1 1 -0.915.9994 4 opls_272 1FMT O2 1 -0.915.9994 5 MW 1FMT D 10.0 12.011 Should I use some constraints for "dummy mass" to define its position in simulation? And can I get "dummy mass" type from ffoplaa.atp or its better to add the new one? I`m sorry, I`ve read manual and corresponding article but I have not find irrefragable answer for my questions. Thanks Nilov Dmitri > Нилов Дмитрий wrote: > > Thank you very much, but in what way can I define the carbon > > like massless when it treated as a virtual site(type 3) > > in formate molecule? > > You can define it as zero, but take care to get the right moment of > inertia (by defining further virtual sites). > > > Grompp runs with error when carbon has mass: > > > > converting bonded parameters... > > # CONNBONDS: 3 > > # CONSTR: 3 > > # VSITE3: 1 > > Setting particle type to V for virtual sites > > ERROR 2 [file "fmt.top", line 82]: > > virtual site C (Res FMT-1) has non-zero mass 12.011 > > - > > > > -Original Message- > >> Нилов Дмитрий wrote: > >>> Hello! > >>> I would like to involve formate molecule (HCOO-)in my dynamics, but I > >>> have the problem when I use virtual site (type 3fd)for it. > >>> > >>> When I run grompp for single formate molecule, it`s ok. > >>> But after solvating in bath of solvent (tip3p) grompp runs with error: > >> In this case you would be best off defining three constraints from > >> H O1 > >> H O2 > >> O1 O2 > >> and define the carbon as a virtual site defined by the plane (check > >> TIP4P topology). > -- > David van der Spoel, Ph.D. ___ 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] Virtual site and constraints
Нилов Дмитрий wrote: OK, could I add "dummy mass" that has coordinates and mass such as carbon to keep right moment of inertia? I mean something like this: [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1FMT H 1 0.22 1.008 2 opls_271 1FMT C 1 0.58 0.000 3 opls_272 1FMT O1 1 -0.915.9994 4 opls_272 1FMT O2 1 -0.915.9994 5 MW 1FMT D 10.0 12.011 Should I use some constraints for "dummy mass" to define its position in simulation? And can I get "dummy mass" type from ffoplaa.atp or its better to add the new one? Have you tried naming it an atom instead of a virtual site? I`m sorry, I`ve read manual and corresponding article but I have not find irrefragable answer for my questions. Thanks Nilov Dmitri Нилов Дмитрий wrote: Thank you very much, but in what way can I define the carbon like massless when it treated as a virtual site(type 3) in formate molecule? You can define it as zero, but take care to get the right moment of inertia (by defining further virtual sites). Grompp runs with error when carbon has mass: converting bonded parameters... # CONNBONDS: 3 # CONSTR: 3 # VSITE3: 1 Setting particle type to V for virtual sites ERROR 2 [file "fmt.top", line 82]: virtual site C (Res FMT-1) has non-zero mass 12.011 - -Original Message- Нилов Дмитрий wrote: Hello! I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it. When I run grompp for single formate molecule, it`s ok. But after solvating in bath of solvent (tip3p) grompp runs with error: In this case you would be best off defining three constraints from H O1 H O2 O1 O2 and define the carbon as a virtual site defined by the plane (check TIP4P topology). -- David van der Spoel, Ph.D. ___ 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 -- 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 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] deshuf.ndx doesn't work for forces?
Hello All, I found sth like a bug regarding the deshuffle index file. I did a simulation using multiple cpus and -sort -shuffle options. After that I tried to use the deshuf.ndx file to recover the original atom order for my trr file by trjconv -n deshuf.ndx ... command. But by checking the output trr using the gmxdump, I found the oders of x and v were deshuffled while the f oder remained unchanged. In another word the values of forces were not consistent with those of positions and velocities in the new trr file. Is this a bug? And is there anyway to get the correct oder for forces also? Thanks a lot. Lanyuan Lu _ 手机也能上 MSN 聊天了，快来试试吧！ http://mobile.msn.com.cn/ ___ 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] polyatomic ion additon by genion
I tried with genbox option with perticular concentration i.e. perticular number of each component like guanidium ion thiocynate ion & water molecule. But while doing PR(position restrain MD) it showing errors : constraints errors in algorithm shake at step 0. t=o.oo ps : water molecule starting at atom 3010 can not be settled. check for bad contacts and/or reduce the time steps. i reduced the time steps in pr.mdp from .002 to .001 ps file but again it shows the same problem.i have seen the pdb files after genbox really some close contacts between was there it means insertion of extra molecule by gen box is not proper it leads to some bad contacts. The real problem is that when performing simulation of peptide with guanidium ion , CL- , water it is showing no problem because CL- is added in genion steps. Only change in new system (guanidium ion, SCN- , water, peptide) is of SCN-. Addition of SCN- in genbox step is creating problem. Is any other method to perform simulation of peptide in solvent systrm (guanidium ion, SCN-, water). Please give me some insight to resolve this issue. This is pr.mdp file title = Nanomer ; a string cpp = /lib/cpp ; c-preprocessor define = -DPOSRES dt = 0.001; time step integrator = md tinit = 0.0 nsteps = 10 ; number of steps nstcomm = 1; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstfout = 0 nstlog = 500 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ; Neighbour Searching ns_type = grid ; pairlist method ; Electrostatics and VdW coulombtype = PME vdwtype = shift rlist = 1.5 ; cut-off for ns rvdw_switch = 0.8 rvdw= 1.4 ; cut-off for vdw rcoulomb_switch = 0.8 rcoulomb= 1.5 ; cut-off for coulomb ;Temperature coupling Tcoupl = berendsen; temperature bath (yes,no) ref_t = 298 298 tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ; Pressure coupling Pcoupl = no ; pressure bath tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Velocity generation gen_vel = yes ; generate initial gen_temp= 298.0; initial temperature gen_seed= 173529 ; random seed constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 > [EMAIL PROTECTED] wrote: >> Hi all, >> >> I have been trying to simulate peptide in water box with guanidium ion >> & >> thiocynate ion(SCN-).I tried to add these ion by genion command line by >> simply adding topology information of these ion in ions.itp of gromacs >> library directory but it is not working properly it only adds one atom >> by replacing water molecule it seems that genion is applicable only for >> monoatomic ion. >> If i have to do simulation with these polyatomic ions with perticular >> salt concentration how do i will perform it. >> > with genbox. compute number yourself. >> >> Kinshuk >> IIT-Bombay >> India >> >> ___ >> 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 > > > -- > David van der Spoel, Ph.D. > 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 th
Re: [gmx-users] deshuf.ndx doesn't work for forces?
LuLanyuan wrote: > Hello All, > I found sth like a bug regarding the deshuffle index file. I did a simulation > using multiple cpus and -sort -shuffle options. After that I tried to use the > deshuf.ndx file to recover the original atom order for my trr file by trjconv > -n deshuf.ndx ... command. But by checking the output trr using the gmxdump, > I found the oders of x and v were deshuffled while the f oder remained > unchanged. In another word the values of forces were not consistent with > those of positions and velocities in the new trr file. > Is this a bug? And is there anyway to get the correct oder for forces also? Sounds like a bug. The only way is to edit src/tools/gmx_trjconv.c. Please file a bugzilla with an appropriate patch. > Thanks a lot. > Lanyuan Lu > _ > 手机也能上 MSN 聊天了，快来试试吧！ > http://mobile.msn.com.cn/ > ___ > 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 -- David van der Spoel, Ph.D. 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
