[gmx-users] g_msd ?
Hi # g_msd_mpi is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title Diffusion Coefficients / Molecule @xaxis label Molecule @yaxis label D @TYPE xy 00.907803 1 3.5355 2 4.34231 3 3.83589 xaxis = Molecule # from .top file yaxis = diffusion coefficient 1. what does the first row represent ? ( Molecule # = 0 ??? ) 2. what is the unit for the diffusion coefficient ?? 3. why are the diffusion coefficients quite different for the same type of molecules ( water ) ?? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dssp programm
Hello I installed the dssp program for obtaining the secondary structure.I used the dssp programm to analyze the secondary structure of the protein after a MD simulation run. I got the out of the pogramm as m.dssp but I want to know how do I represent the output of the dssp programm graphically or how do I visualize the output of the dssp programm. regards subarna Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with metals GROMACS/CPMD
Hi, This error has origin in the Gromacs part of the QMMM interface. If you can send me the index.ndx, .gro, and CPMD_inp.run files, I might figure out what's going on. -pb. On Fri, Sep 11, 2009 at 11:38 AM, jorge_quint...@ciencias.uis.edu.cowrote: Hello all. I have tried to perfomed some simulations about protein dynamics, including one copper ion around the protein by Gromacs/CPMD. However, I get some problems during CPMD simulation. In the *.mdp file I added the following: QMMM= yes QMmethod= CPMD QMMMscheme = normal QMMM-grps = QM QMbasis = STO-3G planewavecutoff = 40 qmmmcoul_cutoff = 40 qmbox_cpmd = 40.0 40.0 40.0 ; QM charge QMcharge = 2 ; QM multiplicity QMmult = 1 ; Surface Hopping In the CPMD_inp.tmpl file I added: CPMD INTERFACE GMX MOLECULE CENTER OFF END DFT FUNCTIONAL LDA END SYSTEM SYMMETRY 0 CELL 30.0 1.0 1.0 0.0 0.0 0.0 CUTOFF 110.0 CHARGE 2 END ATOMS *H_VDB.uspp BINARY NEWF TPSEU LMAX=S *C_VDB.uspp BINARY NEWF TPSEU LMAX=P *O_VDB.uspp BINARY NEWF TPSEU LMAX=P *N_VDB.uspp BINARY NEWF TPSEU LMAX=P *Cu_VDB.uspp BINARY NEWF TPSEU LMAX=D LOCAL=P END --- During my simulation I get the above message: * ATOMS NR TYPEX(bohr)Y(bohr)Z(bohr) MBL 1 H 21.823587 25.130608 15.200097 3 2 H 24.280230 24.280222 13.688314 3 3 H 20.236217 24.223539 11.458441 3 4 H 22.082445 21.459965 11.112804 3 5 H 17.140066 21.209700 12.743852 3 6 H 14.522986 19.494656 19.351984 3 7 H 15.663084 23.637722 25.007776 3 8 H 11.751351 25.036116 22.891285 3 9 H 11.789140 23.581034 18.091379 3 10 H 24.969240 15.511571 28.327412 3 11 H 23.656624 18.214203 29.448629 3 12 H 24.922737 20.670853 25.782564 3 13 H 26.491213 18.081922 24.459755 3 14 H 27.596189 19.481304 27.288034 3 15 H 20.372282 15.476724 27.237070 3 16 H 21.691307 22.466095 21.492886 3 17 C 21.011011 22.598375 12.478894 3 18 C 18.800028 21.181072 13.688314 3 19 C 15.058371 21.502331 19.338598 3 20 C 15.133955 22.976320 23.155846 3 21 C 13.111957 23.127495 19.584265 3 22 C 24.091259 17.212650 27.710081 3 23 C 25.924290 18.951195 26.254995 3 24 C 21.483442 16.815811 26.425072 3 25 O 19.102385 20.141733 15.767013 3 26 O 20.840929 18.214203 24.629829 3 27 N 22.692860 23.562132 14.482003 3 28 N 16.683536 22.503889 21.190529 3 29 N 12.998570 23.826700 22.078703 3 30 Cu 21.011011 22.598375 12.478894 3 31 Cu 18.800028 21.181072 13.688314 3 32 Cu 15.058371 21.502331 19.338598 3 33 Cu 15.133955 22.976320 23.155846 3 34 Cu 13.111957 23.127495 19.584265 3 35 Cu 24.091259 17.212650 27.710081 3 36 Cu 25.924290 18.951195 26.254995 3 37 Cu 21.483442 16.815811 26.425072 3 ATOM TYPE= 2 NUM= 1 21.01101110005 22.5983753000112.47889420001 ATOM TYPE= 5 NUM= 1 21.01101110005 22.5983753000112.47889420001 PROGRAM STOPS IN SUBROUTINE SETSYS| ATOMS ARE VERY CLOSE STOP 999 --- I worked only with one copper, but in the CPMD_inp.run file appears multiple copper atoms. Any suggestion about that. Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] pdb2gmx bug?
Hi all, I'm trying to convert a .pdb file to a .gro file and the corresponding .top using pdb2gmx. The .pdb contains three subunits. The subunits are all the same protein, however each one is a different length (I'm assuming this is due to the experiment because that's how the file came from pdb.org). Other than that, the subunits are identical (i.e. identical sequences). I start pdb2gmx with this command: pdb2gmx -f tri_ABC.pdb -o tri_ABC -p tri_ABC -i tri_ABC -ignh -ff G53a6 I then get the following warnings: WARNING: atom CG is missing in residue GLN 111 in the pdb file WARNING: atom CD is missing in residue GLN 111 in the pdb file WARNING: atom OE1 is missing in residue GLN 111 in the pdb file WARNING: atom NE2 is missing in residue GLN 111 in the pdb file WARNING: atom HE21 is missing in residue GLN 111 in the pdb file You might need to add atom HE21 to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) WARNING: atom HE22 is missing in residue GLN 111 in the pdb file You might need to add atom HE22 to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) There were 6 missing atoms in molecule Protein_A Now here's where it gets wierd. Residue 111 in all three subunits of my protein is SER, not GLN. I have no idea where the program is getting GLN, but it's only complaining about the 'extra' atoms that GLN has, but SER doesn't. When I use the -missing option, I get a structure and a topology file that look ok. I do, however get similar warnings from the other two subunits. I end up with a total of 6 residues from the three subunits that pdb2gmx can't find atoms from because they are not the same residues as in my pdb. Has anyone seen this before? Any ideas as to what could be causing this, or is it maybe a bug? Thanks for your help Gard Nelson ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PMF of helix dimer
I am performing PMF calculations for my helix dimer using umbrella potential and WHAM analysis. I have already obtained the main reaction coordinates and have divided my path into several windows. From each of this windows, corresponding to a specified distance between my two dimers, I am simulating 400 ps in order to obtain the entry files for g_wham. I have observed, although, that my structures do not stay within the specified distance. The two monomers fall back onto each other, as one would expect happening. I have read that this sampling windows must be in equilibrium, i.e., both monomers should remain where they are in order to get a good overlap between windows. Will that be a problem later on when I try to do my wham analysis? Thank you Fabrício Bracht ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xyz2pdb Fortran File
Hello Gromacs Users, I just wanted to share with you a simple fortran program I wrote that reads a .xyz file and outputs a .pdb file. I'm sure some of you will find it useful. Chris Rowan *** * This program reads a .xyz file and prints out the .pdb * * file. * * * * Execute with ./xyz2pdb input.xyz * * * * Writtten by Christopher K. Rowan September 1, 2009 * * University of Victoria, B.C. Canada * *** implicit real*8(a-h,o-z) character*2 atom character (LEN=6) :: hetatm = HETATM * Edit line below for residue name character (LEN=3) :: res = RES * Unimportant numbers go here: character (LEN=9) :: unknown1 = 1 character (LEN=13) :: unknown2 = 1.00 20.00 * Edit the pdb file name below: open(unit=1,file=output.pdb) read(*,*)n read(*,*) do i=1,n read(*,*)atom,x,y,z write(1,500)hetatm,i,atom,res,unknown1,x,y,z,unknown2 enddo 500 format(a6,i5,a4,a5,a9,3f8.3,a13) end ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] autocorrelation function using g_analyze
Hello, Does anyone know exactly how g_analyze -ac calculates autocorrelation function? My input file, dist.xvg, contains a distance d(t) between two specific atoms of my molecule in time t. (hence d(t)0) I calculated the autocorrelation function using the following command: g_analyze -f dist.xvg -ac corr-dist.xvg What I don't understand is that the correlation function C(k) in the output file, corr-dis.xvg, includes some negative values and even goes down to almost -0.5! I thought by definition the autocorrelation function C(t) is calculated as following: C(k) = d(t)*d(t+k) where C(k) should be always positive because d(t), distance, is always positive in this case. So does anybody know precisely what formula g_analyze -ac uses to calculate the autocorrelation function? Thank you very much for your help in advance. Regards, Sung ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] No default Angle types
Dear GROMACS Gurus, I received the following error when running grompp: / ERROR 0 [file graphene.top, line 392284]: No default Angle types / I believe this error is referring to the fact that there was no definition of an angle type for the following combination of atoms: HA CA CT since line 392284 of the top file has this combination of atoms. I took a look through the ffoplsaabon.itp file and saw that indeed there was no definition for an angle between this combination of atoms. So I thought that I could resolve this error by copying the ffoplsaabon.itp file into my working directory, making a copy of the line for the CA CA HA and renaming the combination CT CA HA. However, when I ran grompp again, I still get the same error. Please advise. Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spacing distance in tabulated angle interaction function
Dear GMXers, I want to use tabulated interaction functions for bonds and angles. According to the manual, f(x) and f'(x) should be computed as functions of x in spacing distance of dx. For bonds, the spacing distance can be set as 0.002 (in single precision) at default. But for angles, what shoud be set for the spacing distance? Please give me some hints. Thanks a lot for your attention! Sincerely, Chaofu Wu, Dr. _ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems with DNA simulation
Hi. I am new to Gromacs and I am following the tutorial on http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I have managed to get the DNA into a water box. When I run genbox I use the ffamber_tip4p.gro water model. When I then run: grompp -f neutralize.mdp -c solved.pdb -p topol I get this fatal error: where neutralize.mdp is from the website above. --- Program grompp, VERSION 4.0.5 Source code file: readir.c, line: 1463 Fatal error: Invalid T coupling input: 0 groups, 2 ref_t values and 2 tau_t values --- I have been searching for an explanation to this error but haven't found anything. Can somone please help. Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] autocorrelation function using g_analyze
Sung Hyun Park wrote: Hello, Does anyone know exactly how g_analyze -ac calculates autocorrelation function? My input file, dist.xvg, contains a distance d(t) between two specific atoms of my molecule in time t. (hence d(t)0) I calculated the autocorrelation function using the following command: g_analyze -f dist.xvg -ac corr-dist.xvg What I don't understand is that the correlation function C(k) in the output file, corr-dis.xvg, includes some negative values and even goes down to almost -0.5! I thought by definition the autocorrelation function C(t) is calculated as following: C(k) = d(t)*d(t+k) where C(k) should be always positive because d(t), distance, is always positive in this case. So does anybody know precisely what formula g_analyze -ac uses to calculate the autocorrelation function? They're described in the manual in one of the appendices. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dssp programm
subarna thakur wrote: Hello I installed the dssp program for obtaining the secondary structure.I used the dssp programm to analyze the secondary structure of the protein after a MD simulation run. I got the out of the pogramm as m.dssp but I want to know how do I represent the output of the dssp programm graphically or how do I visualize the output of the dssp programm. If you are using dssp as a standalone executable, you'll just get a text file with some statistics. If you want the nice pictures you see in publications, you have to use do_dssp, which acts as an interface to dssp, and can be used with trajectories. -Justin regards subarna Connect more, do more and share more with Yahoo! India Mail. Learn more http://in.rd.yahoo.com/tagline_galaxy_3/*http://in.overview.mail.yahoo.com/. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_msd ?
Chih-Ying Lin wrote: Hi # g_msd_mpi is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title Diffusion Coefficients / Molecule @xaxis label Molecule @yaxis label D @TYPE xy 00.907803 1 3.5355 2 4.34231 3 3.83589 xaxis = Molecule # from .top file yaxis = diffusion coefficient 1. what does the first row represent ? ( Molecule # = 0 ??? ) Indexing starts from zero, probably. 2. what is the unit for the diffusion coefficient ?? g_msd should have printed an average value of D, complete with units. 3. why are the diffusion coefficients quite different for the same type of molecules ( water ) ?? Probably due to poor statistics. Individual diffusion coefficients are usually less interesting than averaged behavior. -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with DNA simulation
Gunnar Widtfeldt Reginsson wrote: Hi. I am new to Gromacs and I am following the tutorial on http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I have managed to get the DNA into a water box. When I run genbox I use the ffamber_tip4p.gro water model. When I then run: grompp -f neutralize.mdp -c solved.pdb -p topol I get this fatal error: where neutralize.mdp is from the website above. --- Program grompp, VERSION 4.0.5 Source code file: readir.c, line: 1463 Fatal error: Invalid T coupling input: 0 groups, 2 ref_t values and 2 tau_t values --- I have been searching for an explanation to this error but haven't found anything. Can somone please help. Not without seeing the relevant section of your .mdp file, but it looks like you haven't actually specified any groups to be subject to temperature coupling. -Justin Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs site down?
Hello, I'm currently not able to reach the www.gromacs.org site. While trying to do so, I receive the following: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status Code: 0 Does someone experience the same problem? Regards, Max P.S. I'm running a debian/unstable box, with apache2 (version 2.2.13-2) installed, if this matters -- *** Latevi Max LAWSON DAKU Departement de chimie physique Universite de Geneve - Sciences II 30, quai Ernest-Ansermet CH-1211 Geneve 4 Switzerland Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 *** ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs site down?
Latévi Max LAWSON DAKU wrote: Hello, I'm currently not able to reach the www.gromacs.org site. While trying to do so, I receive the following: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status Code: 0 Does someone experience the same problem? Yes, this is correct. Don't know why, but probably tomorrow it will be fixed. Regards, Max P.S. I'm running a debian/unstable box, with apache2 (version 2.2.13-2) installed, if this matters -- 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. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs site down?
On 20. 09. 09 17:52, David van der Spoel wrote: Latévi Max LAWSON DAKU wrote: Hello, I'm currently not able to reach the www.gromacs.org site. While trying to do so, I receive the following: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status Code: 0 Does someone experience the same problem? Yes, this is correct. Don't know why, but probably tomorrow it will be fixed. Thanks a lot, David, for your answer. Max Regards, Max P.S. I'm running a debian/unstable box, with apache2 (version 2.2.13-2) installed, if this matters -- *** Latevi Max LAWSON DAKU Departement de chimie physique Universite de Geneve - Sciences II 30, quai Ernest-Ansermet CH-1211 Geneve 4 Switzerland Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 *** ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: autocorrelation function using g_analyze
They're described in the manual in one of the appendices. Mark Dear Mark, Thank you so much for your reply. I just checked the manual again and looked through the appendices, but could not find the exact formula used by gromacs to calculate the autocorrelation function in g_analyze. I'm sorry to bother you again but could you tell me more specifically where to look in the appendices? I also checked the special topics chapter in the manual but it is still not clear to me which equation is being used by gromacs. Thanks in advance for your help! Regards, Sung ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] molecule index
Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Many Thanks in advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: autocorrelation function using g_analyze
Sung Hyun Park wrote: They're described in the manual in one of the appendices. Mark Dear Mark, Thank you so much for your reply. I just checked the manual again and looked through the appendices, but could not find the exact formula used by gromacs to calculate the autocorrelation function in g_analyze. I'm sorry to bother you again but could you tell me more specifically where to look in the appendices? I also checked the special topics chapter in the manual but it is still not clear to me which equation is being used by gromacs. I would suggest section 8.5 Correlation functions to get the overview of these calculations, and any special forms that might be used be certain programs. -Justin Thanks in advance for your help! Regards, Sung ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] who can help me with the force-field?
Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Missing Residues
Hi All, My protein has lots of missing residues and in every chain there are 4-5 missing residues with atom name. I can see missing residues with the help of Swiss PDB Viewer after I load the pdb file. I am very new in Swiss PDB viewer and I would highly appreciate if anyone can let me know how to fix the missing residues or add the missing residues in the original PDB file using swiss pdb viewes before I start my simulations in GROMACS. Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Missing Residues
sunny mishra wrote: Hi All, My protein has lots of missing residues and in every chain there are 4-5 missing residues with atom name. I can see missing residues with the help of Swiss PDB Viewer after I load the pdb file. I am very new in Swiss PDB viewer and I would highly appreciate if anyone can let me know how to fix the missing residues or add the missing residues in the original PDB file using swiss pdb viewes before I start my simulations in GROMACS. If you save the layer in Swiss PDBViewer, the .pdb file will contain the missing atoms that have been added. Missing residues are entirely different issue. You will have to use a program like Modeller or Loopy to re-build any missing residues. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] molecule index
Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Try it and see. One of these sets of numbers is larger than the other, and if you use a number in that interval you'll either get an error or success, either of which will answer your question. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] who can help me with the force-field?
xiao shijun wrote: Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! Usually you would not define a nonbonded interaction for atoms that are so close together, since their interaction should be able to be modelled adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, an interaction harmonic the O-O distance as a Urey-Bradley term). Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: autocorrelation function using g_analyze
Justin A. Lemkul wrote: Sung Hyun Park wrote: They're described in the manual in one of the appendices. Mark Dear Mark, Thank you so much for your reply. I just checked the manual again and looked through the appendices, but could not find the exact formula used by gromacs to calculate the autocorrelation function in g_analyze. I'm sorry to bother you again but could you tell me more specifically where to look in the appendices? I also checked the special topics chapter in the manual but it is still not clear to me which equation is being used by gromacs. I would suggest section 8.5 Correlation functions to get the overview of these calculations, and any special forms that might be used be certain programs. Indeed. The key bit of information not explicitly stated in 8.5, but present in g_analyze -h, is that normalization is on by default. The correlation function is only dimensionless if it has been normalized (subtract mean from all data points, divide by standard deviation). A normalized correlation function can readily be negative - consider the correlation of two fully-out-of-phase sinusoids. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] spacing distance in tabulated angle interaction function
wuxiao wrote: Dear GMXers, I want to use tabulated interaction functions for bonds and angles. According to the manual, f(x) and f'(x) should be computed as functions of x in spacing distance of dx. For bonds, the spacing distance can be set as 0.002 (in single precision) at default. But for angles, what shoud be set for the spacing distance? Please give me some hints. Thanks a lot for your attention! It barely matters :-) GROMACS is probably using the difference between adjacent values of the derivatives to estimate the second derivative for a second-order Taylor expansion, and so as long as the spacing is small enough that this estimate is valid, you're fine. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No default Angle types
Darrell Koskinen wrote: Dear GROMACS Gurus, I received the following error when running grompp: / ERROR 0 [file graphene.top, line 392284]: No default Angle types / I believe this error is referring to the fact that there was no definition of an angle type for the following combination of atoms: HA CA CT since line 392284 of the top file has this combination of atoms. I took a look through the ffoplsaabon.itp file and saw that indeed there was no definition for an angle between this combination of atoms. So I thought that I could resolve this error by copying the ffoplsaabon.itp file into my working directory, making a copy of the line for the CA CA HA and renaming the combination CT CA HA. However, when I ran grompp again, I still get the same error. Please advise. Yes I believe that should work. You could also add a new [angletypes] directive into your .top file after the forcefield files to define this angle type. That might avoid any problems with ffoplsaa.itp needing to include the version of ffoplsaabon.itp local to your .top file rather than local to itself (if that's what's happening). Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx bug?
Gard Nelson wrote: Hi all, I'm trying to convert a .pdb file to a .gro file and the corresponding .top using pdb2gmx. The .pdb contains three subunits. The subunits are all the same protein, however each one is a different length (I'm assuming this is due to the experiment because that's how the file came from pdb.org http://pdb.org). Other than that, the subunits are identical (i.e. identical sequences). I start pdb2gmx with this command: pdb2gmx -f tri_ABC.pdb -o tri_ABC -p tri_ABC -i tri_ABC -ignh -ff G53a6 No you're not converting a .pdb to a .gro file (which you don't ever need to do for normal usage), you are generating a molecular topology. Also you should probably read the paper and/or comments associated with the .pdb file to understand the reason for the different lengths :-) I then get the following warnings: WARNING: atom CG is missing in residue GLN 111 in the pdb file WARNING: atom CD is missing in residue GLN 111 in the pdb file WARNING: atom OE1 is missing in residue GLN 111 in the pdb file WARNING: atom NE2 is missing in residue GLN 111 in the pdb file WARNING: atom HE21 is missing in residue GLN 111 in the pdb file You might need to add atom HE21 to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) WARNING: atom HE22 is missing in residue GLN 111 in the pdb file You might need to add atom HE22 to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) There were 6 missing atoms in molecule Protein_A Now here's where it gets wierd. Residue 111 in all three subunits of my protein is SER, not GLN. I have no idea where the program is getting GLN, but it's only complaining about the 'extra' atoms that GLN has, but SER doesn't. Where's the nearest GLN? Mark When I use the -missing option, I get a structure and a topology file that look ok. I do, however get similar warnings from the other two subunits. I end up with a total of 6 residues from the three subunits that pdb2gmx can't find atoms from because they are not the same residues as in my pdb. Has anyone seen this before? Any ideas as to what could be causing this, or is it maybe a bug? Thanks for your help Gard Nelson ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with grompp , ffamber99 and ions
Hi.I am trying to run this command on a solvated DNA grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx and I get this fatal error: --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Na+ --- I have added to the file ions.itp : [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1amber99_31 1 Na+ Na 1 1 because this is how the Na ion is in ffamber99.rtp [ Na+ ] [ atoms ] Na amber99_31 1.0 1 And this I have done according to the amber website: http://chemistry.csulb.edu/ffamber/#aadat The last part of the topol.top file is: SOL 13651 Na+ 38 Cl 0 and the structure file contains: ATOM 55905 Na Na+ 3729 77.070 47.215 21.822 1.00 0.00 Does anyone know what could be wrong? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with grompp , ffamber99 and ions
Gunnar Widtfeldt Reginsson wrote: Hi. I am trying to run this command on a solvated DNA grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx and I get this fatal error: --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Na+ --- I have added to the file ions.itp : [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1amber99_31 1 Na+ Na 1 1 because this is how the Na ion is in ffamber99.rtp Did you do #include ions.itp ? Mark [ Na+ ] [ atoms ] Na amber99_31 1.0 1 And this I have done according to the amber website: http://chemistry.csulb.edu/ffamber/#aadat The last part of the topol.top file is: SOL 13651 Na+ 38 Cl 0 and the structure file contains: ATOM 55905 Na Na+ 3729 77.070 47.215 21.822 1.00 0.00 Does anyone know what could be wrong? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] molecule index
Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. Fatal error: The index group does not consist of whole molecules I also did not understand what you pointed out about One of these sets of numbers is larger than the other ... questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say g_msd -n index and did not explain which index... how about if I use oxygen.ndx file?? I really appreciate your help. Many Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Try it and see. One of these sets of numbers is larger than the other, and if you use a number in that interval you'll either get an error or success, either of which will answer your question. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with grompp , ffamber99 and ions
Gunnar Widtfeldt Reginsson wrote: Hi. I am trying to run this command on a solvated DNA grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx and I get this fatal error: --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Na+ --- I have added to the file ions.itp : [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1amber99_31 1 Na+ Na 1 1 Is this section contained in an appropriate #ifdef _FF_AMBER block? -Justin because this is how the Na ion is in ffamber99.rtp [ Na+ ] [ atoms ] Na amber99_31 1.0 1 And this I have done according to the amber website: http://chemistry.csulb.edu/ffamber/#aadat The last part of the topol.top file is: SOL 13651 Na+ 38 Cl 0 and the structure file contains: ATOM 55905 Na Na+ 3729 77.070 47.215 21.822 1.00 0.00 Does anyone know what could be wrong? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] molecule index
Jamie Seyed wrote: Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. Fatal error: The index group does not consist of whole molecules OK so apparently it wants atom indices for whole molecules. That seems much more plausible to me than David's advice you quoted (please give URLs to such quotes in future, perhaps you took it out of context...) So try giving it atom indices for a whole water molecule as an experiment. Seems like an obvious try to me :-) Then, scale it up if it seems to work. I also did not understand what you pointed out about One of these sets of numbers is larger than the other ... One of the set of atom indices in a protein and the set of molecule indices in a solvated protein will have more members than the other. Instead of asking which is right, you might try out a case that will fail under one assumption and work under the other :-) Then perhaps ask a question with some evidence behind it. questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say g_msd -n index and did not explain which index... how about if I use oxygen.ndx file?? Provide links, please. We're not going to duplicate your googling. Mark I really appreciate your help. Many Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Try it and see. One of these sets of numbers is larger than the other, and if you use a number in that interval you'll either get an error or success, either of which will answer your question. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] molecule index
Thanks Mark, here are the links. http://www.psc.edu/general/software/packages/gromacs/online/water.html http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html I tried your advice with 1 water molecule and since it worked I tried it with SOL.ndx, but I got D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s It seems not reasonable to me (negative and its error is bigger than itself). Any idea? Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. Fatal error: The index group does not consist of whole molecules OK so apparently it wants atom indices for whole molecules. That seems much more plausible to me than David's advice you quoted (please give URLs to such quotes in future, perhaps you took it out of context...) So try giving it atom indices for a whole water molecule as an experiment. Seems like an obvious try to me :-) Then, scale it up if it seems to work. I also did not understand what you pointed out about One of these sets of numbers is larger than the other ... One of the set of atom indices in a protein and the set of molecule indices in a solvated protein will have more members than the other. Instead of asking which is right, you might try out a case that will fail under one assumption and work under the other :-) Then perhaps ask a question with some evidence behind it. questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say g_msd -n index and did not explain which index... how about if I use oxygen.ndx file?? Provide links, please. We're not going to duplicate your googling. Mark I really appreciate your help. Many Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Try it and see. One of these sets of numbers is larger than the other, and if you use a number in that interval you'll either get an error or success, either of which will answer your question. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] molecule index
Jamie Seyed wrote: Thanks Mark, here are the links. http://www.psc.edu/general/software/packages/gromacs/online/water.html http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html I tried your advice with 1 water molecule and since it worked I tried it with SOL.ndx, but I got D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s It seems not reasonable to me (negative and its error is bigger than itself). Any idea? Probably inadequate sampling, either from the number of frames saved, or from the length of the simulation itself. -Justin Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. Fatal error: The index group does not consist of whole molecules OK so apparently it wants atom indices for whole molecules. That seems much more plausible to me than David's advice you quoted (please give URLs to such quotes in future, perhaps you took it out of context...) So try giving it atom indices for a whole water molecule as an experiment. Seems like an obvious try to me :-) Then, scale it up if it seems to work. I also did not understand what you pointed out about One of these sets of numbers is larger than the other ... One of the set of atom indices in a protein and the set of molecule indices in a solvated protein will have more members than the other. Instead of asking which is right, you might try out a case that will fail under one assumption and work under the other :-) Then perhaps ask a question with some evidence behind it. questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say g_msd -n index and did not explain which index... how about if I use oxygen.ndx file?? Provide links, please. We're not going to duplicate your googling. Mark I really appreciate your help. Many Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Try it and see. One of these sets of numbers is larger than the other, and if you use a number in that interval you'll either get an error or success, either of which will answer your question. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella potential
I have performed a series of umbrella sampling simulations in order to do a WHAM analysis. The profile.xvg file I obtain is a continuous descending line along my distance axis. There is no increase in energy after my two structures separate. Perhaps I am doing something wrong. Thank you ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella potential
Stefan Hoorman wrote: I have performed a series of umbrella sampling simulations in order to do a WHAM analysis. The profile.xvg file I obtain is a continuous descending line along my distance axis. There is no increase in energy after my two structures separate. Perhaps I am doing something wrong. Sounds like it, but there's no way anyone on this list will know that unless you describe your system in greater detail - how you generated the starting configurations, how many windows you used and what distances that corresponds to, the pull parameters you've specified in your .mdp file, and anything else that might be pertinent. -Justin Thank you ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] molecule index
Yes Thanks Justin, should I just use the linear part of msd for fit even if it is short (like 14ps from 200ps)? Thanks/Jamie On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Thanks Mark, here are the links. http://www.psc.edu/general/software/packages/gromacs/online/water.html http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html I tried your advice with 1 water molecule and since it worked I tried it with SOL.ndx, but I got D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s It seems not reasonable to me (negative and its error is bigger than itself). Any idea? Probably inadequate sampling, either from the number of frames saved, or from the length of the simulation itself. -Justin Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. Fatal error: The index group does not consist of whole molecules OK so apparently it wants atom indices for whole molecules. That seems much more plausible to me than David's advice you quoted (please give URLs to such quotes in future, perhaps you took it out of context...) So try giving it atom indices for a whole water molecule as an experiment. Seems like an obvious try to me :-) Then, scale it up if it seems to work. I also did not understand what you pointed out about One of these sets of numbers is larger than the other ... One of the set of atom indices in a protein and the set of molecule indices in a solvated protein will have more members than the other. Instead of asking which is right, you might try out a case that will fail under one assumption and work under the other :-) Then perhaps ask a question with some evidence behind it. questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say g_msd -n index and did not explain which index... how about if I use oxygen.ndx file?? Provide links, please. We're not going to duplicate your googling. Mark I really appreciate your help. Many Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule Would you please clarify this for me?? Try it and see. One of these sets of numbers is larger than the other, and if you use a number in that interval you'll either get an error or success, either of which will answer your question. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org
Re: [gmx-users] molecule index
Jamie Seyed wrote: Yes Thanks Justin, should I just use the linear part of msd for fit even if it is short (like 14ps from 200ps)? Thanks/Jamie Yes, the linear portion of the graph should be used for MSD analysis. 200 ps is somewhat short, but might be sufficient for water. -Justin On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Thanks Mark, here are the links. http://www.psc.edu/general/software/packages/gromacs/online/water.html http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html I tried your advice with 1 water molecule and since it worked I tried it with SOL.ndx, but I got D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s It seems not reasonable to me (negative and its error is bigger than itself). Any idea? Probably inadequate sampling, either from the number of frames saved, or from the length of the simulation itself. -Justin Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. Fatal error: The index group does not consist of whole molecules OK so apparently it wants atom indices for whole molecules. That seems much more plausible to me than David's advice you quoted (please give URLs to such quotes in future, perhaps you took it out of context...) So try giving it atom indices for a whole water molecule as an experiment. Seems like an obvious try to me :-) Then, scale it up if it seems to work. I also did not understand what you pointed out about One of these sets of numbers is larger than the other ... One of the set of atom indices in a protein and the set of molecule indices in a solvated protein will have more members than the other. Instead of asking which is right, you might try out a case that will fail under one assumption and work under the other :-) Then perhaps ask a question with some evidence behind it. questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say g_msd -n index and did not explain which index... how about if I use oxygen.ndx file?? Provide links, please. We're not going to duplicate your googling. Mark I really appreciate your help. Many Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. From David's answer on the list I found - If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109 My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a
[gmx-users] using 'genbox' for adding solvent
Hi everyone, I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named insert.gro which has a single water molecule with the right volume associated with it. But this option gave a segmentation fault and i am not sure why its doing that? May be there's not enough space for additional water but it should not give a segmentation fault for that reason. Is there something wrong with my idea? The insert.gro looks like the following H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984 3 1SOL OW1.130.128.113 1SOLHW12.037.126.150 1SOLHW23.131.089.021 0.31034 0.31034 0.31034 I also tried various other box (larger) sizes for this but it didnt help. Thank you in advance. Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: umbrella potential
Stefan Hoorman wrote: The distances between the two structures in each of the windows are (in nm): 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 1 = 2.66 There is substantial overlap and jumping back and forth (i.e., 1.56, decrease to 1.54, increase to 1.56, then back to 1.52, etc) in these distances, so I think they are not optimal for umbrella sampling. Instead of more regular spacing in time, I would suggest more regular spacing in terms of distance. Most literature on the topic cites how far apart windows were in terms of distance, which is important for WHAM analysis. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using 'genbox' for adding solvent
Amit Choubey wrote: Hi everyone, I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named insert.gro which has a single water molecule with the right volume associated with it. But this option gave a segmentation fault and i am not sure why its doing that? May be there's not enough space for additional water but it should not give a segmentation fault for that reason. Is there something wrong with my idea? A segmentation fault with this approach generally indicates that the requested number of inserted molecules will not fit. Alternately, you can try -cs spc216.gro -maxsol (your number) If the second approach also fails, I would think that would be strong evidence that what you're trying to do won't work. -Justin The insert.gro looks like the following H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984 3 1SOL OW1.130.128.113 1SOLHW12.037.126.150 1SOLHW23.131.089.021 0.31034 0.31034 0.31034 I also tried various other box (larger) sizes for this but it didnt help. Thank you in advance. Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using 'genbox' for adding solvent
I still want to suggest that segmentation fault doesn't occur due to large no. of insertion molecules the reason being that i, once tried to insert only 1 molecule and it came up with seg. fault again . I am very sure that i have space for atleast some(1) no. of water molecules. Amit On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: Hi everyone, I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named insert.gro which has a single water molecule with the right volume associated with it. But this option gave a segmentation fault and i am not sure why its doing that? May be there's not enough space for additional water but it should not give a segmentation fault for that reason. Is there something wrong with my idea? A segmentation fault with this approach generally indicates that the requested number of inserted molecules will not fit. Alternately, you can try -cs spc216.gro -maxsol (your number) If the second approach also fails, I would think that would be strong evidence that what you're trying to do won't work. -Justin The insert.gro looks like the following H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984 3 1SOL OW1.130.128.113 1SOLHW12.037.126.150 1SOLHW23.131.089.021 0.31034 0.31034 0.31034 I also tried various other box (larger) sizes for this but it didnt help. Thank you in advance. Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: umbrella potential
The distances between the two structures in each of the windows are (in nm): 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 1 = 2.66 There is substantial overlap and jumping back and forth (i.e., 1.56, decrease to 1.54, increase to 1.56, then back to 1.52, etc) in these distances, so I think they are not optimal for umbrella sampling. Instead of more regular spacing in time, I would suggest more regular spacing in terms of distance. Most literature on the topic cites how far apart windows were in terms of distance, which is important for WHAM analysis. -Justin Is there a way to do this automatically in gromacs? To extract structures from the simulation based on the distance between them? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using 'genbox' for adding solvent
Amit Choubey wrote: I still want to suggest that segmentation fault doesn't occur due to large no. of insertion molecules the reason being that i, once tried to insert only 1 molecule and it came up with seg. fault again . I am very sure that i have space for atleast some(1) no. of water molecules. Which version of Gromacs are you using? There was a bug in genbox 4.0.3, but was fixed prior to 4.0.4. -Justin Amit On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Hi everyone, I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named insert.gro which has a single water molecule with the right volume associated with it. But this option gave a segmentation fault and i am not sure why its doing that? May be there's not enough space for additional water but it should not give a segmentation fault for that reason. Is there something wrong with my idea? A segmentation fault with this approach generally indicates that the requested number of inserted molecules will not fit. Alternately, you can try -cs spc216.gro -maxsol (your number) If the second approach also fails, I would think that would be strong evidence that what you're trying to do won't work. -Justin The insert.gro looks like the following H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984 3 1SOL OW1.130.128.113 1SOLHW12.037.126.150 1SOLHW23.131.089.021 0.31034 0.31034 0.31034 I also tried various other box (larger) sizes for this but it didnt help. Thank you in advance. Amit ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: umbrella potential
Stefan Hoorman wrote: I have performed a series of umbrella sampling simulations in order to do a WHAM analysis. The profile.xvg file I obtain is a continuous descending line along my distance axis. There is no increase in energy after my two structures separate. Perhaps I am doing something wrong. Sounds like it, but there's no way anyone on this list will know that unless you describe your system in greater detail - how you generated the starting configurations, how many windows you used and what distances that corresponds to, the pull parameters you've specified in your .mdp file, and anything else that might be pertinent. -Justin Ok, I've done the following. I have simulated my system (protein + ligand in water SPC with GROMOS96 53a6 forcefield, with PME, Nose-Hoover thermostat (310 K), parrinello-rahman barostat (1 atm), with the pull code for 15 ns, the pull code content of the mdp file is the following: pull = umbrella pull_geometry = direction pull_dim = Y Y N pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = protein pull_group1 = SLC pull_vec1 = 1 1 0 pull_init1 = 0 pull_rate1 = 0.001 pull_k1 = 35 pull_constr_tol = 1e-06 pull_pbcatom0 = 0 pull_pbcatom1 = 0 Analysing the distance between the groups I get a very shy increase in the initial distance for the first 5 nanoseconds and after that the distance between the two groups increase 5nm in the next 10ns. From this trajectory I have removed 30 structures. The first 10 were obtained with a 500 ps interval between them and the other 20 in 250 ps interval for the next 5ns. The final 5ns of the simulation are not of interest since my Lennard jones and coulomb interaction between the two structures fall to 0 after the first 9 ns of simulation. I then simulated each of these windows for 500 ps with the following mdp_pull content: ; Pull Code pull = umbrella pull_geometry = distance pull_dim = Y Y N pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = protein pull_group1 = SLC pull_vec1 = 1 1 0 pull_init1 = 0 pull_rate1 = 0 pull_k1 = 35 pull_constr_tol = 1e-06 pull_pbcatom0 = 0 pull_pbcatom1 = 0 I have set the pull_geometry to distance since g_wham does not accept direction. The distances between the two structures in each of the windows are (in nm): 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 = 1.52; 2500 = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000 = 1.7; 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 = 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04; 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ; 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 1 = 2.66 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using 'genbox' for adding solvent
yes you are right its a bug, everything works well on the most recent version. Thank you On Sun, Sep 20, 2009 at 6:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: I still want to suggest that segmentation fault doesn't occur due to large no. of insertion molecules the reason being that i, once tried to insert only 1 molecule and it came up with seg. fault again . I am very sure that i have space for atleast some(1) no. of water molecules. Which version of Gromacs are you using? There was a bug in genbox 4.0.3, but was fixed prior to 4.0.4. -Justin Amit On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Amit Choubey wrote: Hi everyone, I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named insert.gro which has a single water molecule with the right volume associated with it. But this option gave a segmentation fault and i am not sure why its doing that? May be there's not enough space for additional water but it should not give a segmentation fault for that reason. Is there something wrong with my idea? A segmentation fault with this approach generally indicates that the requested number of inserted molecules will not fit. Alternately, you can try -cs spc216.gro -maxsol (your number) If the second approach also fails, I would think that would be strong evidence that what you're trying to do won't work. -Justin The insert.gro looks like the following H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984 3 1SOL OW1.130.128.113 1SOLHW12.037.126.150 1SOLHW23.131.089.021 0.31034 0.31034 0.31034 I also tried various other box (larger) sizes for this but it didnt help. Thank you in advance. Amit ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] errors due to genbox
Dear GMXers, I try to generate gro file using genbox, but fail with some errors. Command lines are: genbox -ci B.gro -o Bb.gro -nmol 200 -box 3 3 3 where B.gro is the coordinate file of vinyl alcohol residue. The errors are given as bellows. Please give me some hints to cope with these problem. Thanks a lot for any reply. Sincerely, Chaofu Wu success (now 1400 atoms)!*** glibc detected *** genbox: realloc(): invalid old size: 0x083e6a70 *** === Backtrace: = /lib/libc.so.6[0xb7db8cb1] /lib/libc.so.6[0xb7dbb928] /lib/libc.so.6(__libc_realloc+0x100)[0xb7dbca40] genbox[0x815bd6c] === Memory map: 08048000-083d2000 r-xp 08:09 358678 /usr/local/gromacs/bin/genbox 083d2000-083d9000 rwxp 00389000 08:09 358678 /usr/local/gromacs/bin/genbox 083d9000-21bc3000 rwxp 083d9000 00:00 0 [heap] b7c0-b7c21000 rwxp b7c0 00:00 0 b7c21000-b7d0 ---p b7c21000 00:00 0 b7d5-b7d51000 rwxp b7d5 00:00 0 b7d51000-b7d53000 r-xp 08:09 17118 /lib/libdl-2.4.so b7d53000-b7d55000 rwxp 1000 08:09 17118 /lib/libdl-2.4.so b7d55000-b7e7 r-xp 08:09 17112 /lib/libc-2.4.so b7e7-b7e72000 r-xp 0011a000 08:09 17112 /lib/libc-2.4.so b7e72000-b7e74000 rwxp 0011c000 08:09 17112 /lib/libc-2.4.so b7e74000-b7e77000 rwxp b7e74000 00:00 0 b7e77000-b7f6b000 r-xp 08:09 33645 /usr/X11R6/lib/libX11.so.6.2 b7f6b000-b7f6e000 rwxp 000f4000 08:09 33645 /usr/X11R6/lib/libX11.so.6.2 b7f6e000-b7f6f000 rwxp b7f6e000 00:00 0 b7f6f000-b7f84000 r-xp 08:09 33639 /usr/X11R6/lib/libICE.so.6.4 b7f84000-b7f85000 rwxp 00014000 08:09 33639 /usr/X11R6/lib/libICE.so.6.4 b7f85000-b7f87000 rwxp b7f85000 00:00 0 b7f87000-b7f8f000 r-xp 08:09 33641 /usr/X11R6/lib/libSM.so.6.0 b7f8f000-b7f9 rwxp 7000 08:09 33641 /usr/X11R6/lib/libSM.so.6.0 b7f9-b7fb3000 r-xp 08:09 17120 /lib/libm-2.4.so b7fb3000-b7fb5000 rwxp 00022000 08:09 17120 /lib/libm-2.4.so b7fb5000-b7fc6000 r-xp 08:09 17123 /lib/libnsl-2.4.so b7fc6000-b7fc8000 rwxp 0001 08:09 17123 /lib/libnsl-2.4.so b7fc8000-b7fca000 rwxp b7fc8000 00:00 0 b7fd6000-b7fe2000 r-xp 08:09 331626 /usr/local/lib/libgcc_s.so.1 b7fe2000-b7fe3000 rwxp c000 08:09 331626 /usr/local/lib/libgcc_s.so.1 b7fe3000-b7fe5000 rwxp b7fe3000 00:00 0 b7fe5000-b7fff000 r-xp 08:09 17105 /lib/ld-2.4.so b7fff000-b8001000 rwxp 0001a000 08:09 17105 /lib/ld-2.4.so bffb3000-bffca000 rwxp bffb3000 00:00 0 [stack] e000-f000 ---p 00:00 0 [vdso] Aborted _ 心跳斗地主新版体验，给你360度的心跳体验！ http://club.msn.cn/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] errors due to genbox
On 09/21/09, wuxiao xiaowu...@hotmail.com wrote:
.hmmessage P{margin:0px;padding:0px}body.hmmessage{font-size:
10pt;font-family:Verdana}
Dear GMXers,
I try to generate gro file using genbox, but fail with some errors.
Command lines are:
genbox -ci B.gro -o Bb.gro -nmol 200 -box 3 3 3
where B.gro is the coordinate file of vinyl alcohol residue.
The errors are given as bellows. Please give me some hints to cope with
these problem. Thanks a lot for any reply.
Sincerely,
Chaofu Wu
success (now 1400 atoms)!
All the following material is being generated by the operating system in
response to some failure of GROMACS in allocating memory, or such. Providing
more of the text before here may help developers assess what you're doing wrong.
Mark
*** glibc detected *** genbox: realloc(): invalid old size: 0x083e6a70 ***
=== Backtrace: =
/lib/libc.so.6[0xb7db8cb1]
/lib/libc.so.6[0xb7dbb928]
/lib/libc.so.6(__libc_realloc+0x100)[0xb7dbca40]
genbox[0x815bd6c]
=== Memory map:
08048000-083d2000 r-xp 08:09 358678 /usr/local/gromacs/bin/genbox
083d2000-083d9000 rwxp 00389000 08:09 358678 /usr/local/gromacs/bin/genbox
083d9000-21bc3000 rwxp 083d9000 00:00 0 [heap]
b7c0-b7c21000 rwxp b7c0 00:00 0
b7c21000-b7d0 ---p b7c21000 00:00 0
b7d5-b7d51000 rwxp b7d5 00:00 0
b7d51000-b7d53000 r-xp 08:09 17118 /lib/libdl-2.4.so
b7d53000-b7d55000 rwxp 1000 08:09 17118 /lib/libdl-2.4.so
b7d55000-b7e7 r-xp 08:09 17112 /lib/libc-2.4.so
b7e7-b7e72000 r-xp 0011a000 08:09 17112 /lib/libc-2.4.so
b7e72000-b7e74000 rwxp 0011c000 08:09 17112 /lib/libc-2.4.so
b7e74000-b7e77000 rwxp b7e74000 00:00 0
b7e77000-b7f6b000 r-xp 08:09 33645 /usr/X11R6/lib/libX11.so.6.2
b7f6b000-b7f6e000 rwxp 000f4000 08:09 33645 /usr/X11R6/lib/libX11.so.6.2
b7f6e000-b7f6f000 rwxp b7f6e000 00:00 0
b7f6f000-b7f84000 r-xp 08:09 33639 /usr/X11R6/lib/libICE.so.6.4
b7f84000-b7f85000 rwxp 00014000 08:09 33639 /usr/X11R6/lib/libICE.so.6.4
b7f85000-b7f87000 rwxp b7f85000 00:00 0
b7f87000-b7f8f000 r-xp 08:09 33641 /usr/X11R6/lib/libSM.so.6.0
b7f8f000-b7f9 rwxp 7000 08:09 33641 /usr/X11R6/lib/libSM.so. 6.0
b7f9-b7fb3000 r-xp 08:09 17120 /lib/libm-2.4.so
b7fb3000-b7fb5000 rwxp 00022000 08:09 17120 /lib/libm-2.4.so
b7fb5000-b7fc6000 r-xp 08:09 17123 /lib/libnsl-2.4.so
b7fc6000-b7fc8000 rwxp 0001 08:09 17123 /lib/libnsl-2.4.so
b7fc8000-b7fca000 rwxp b7fc8000 00:00 0
b7fd6000-b7fe2000 r-xp 08:09 331626 /usr/local/lib/libgcc_s.so.1
b7fe2000-b7fe3000 rwxp c000 08:09 331626 /usr/local/lib/libgcc_s.so.1
b7fe3000-b7fe5000 rwxp b7fe3000 00:00 0
b7fe5000-b7fff000 r-xp 08:09 17105 /lib/ld-2.4.so
b7fff000-b8001000 rwxp 0001a000 08:09 17105 /lib/ld-2.4.so
bffb3000-bffca000 rwxp bffb3000 00:00 0 [stack]
e000-f000 ---p 00 00 00:00 0 [vdso]
Aborted
聊天+搜索+邮箱 想要轻松出游,手机MSN帮你搞定! 立刻下载！ (http://mobile.msn.com.cn/)
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: who can help me with the force-field?
Mark wrote: xiao shijun wrote: Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! Usually you would not define a nonbonded interaction for atoms that are so close together, since their interaction should be able to be modelled adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, an interaction harmonic the O-O distance as a Urey-Bradley term). Thanks for Mark's suggestion. But I want to reproduce the simulation from the other paper, The paper describe the force-field that O-O nonbonded interaction in the same carbonate should be considered. In addition to that, I can't use buckingham potential in [pairs], even choose funct = 2. I am wondering if I want to describe 1-4 interaction by Buckingham, what could I do? BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
