[gmx-users] [Fwd: gen_seed GROMACS]
Original Message Subject: gen_seed GROMACS Date: Sun, 3 Sep 2006 19:36:35 -0700 (PDT) From: Fenghui Fan [EMAIL PROTECTED] To: [EMAIL PROTECTED] Will you please give me an explaination on gen_seed? How can we decide its value? How does it influence the final resuts? What is getpid? I am looking forward to getting your reply. Best regards. Fenghui Fan __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] invacuo simulation
Dear gmx users, I am working on protein invacuo simulation in different condition like considering different box size (0.7, 0.8, 1.0) and also with and without pressure coupling. When I am looking at the rmsd and gyration results, they are all varying alot for all the simulations. The simulation seem to be equilibrated for a certain time and then but again they start deviating. I dont have any clue for why the system is showing a lot of discrepancies with in different simulations when they differ only in the box size. Can some on through some light on it? regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Tip5p with gromos 96, error atom has mass 0
Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file,three errors came even the system just have one tip5p water. The error is : ERROR 1 [file "topol.top", line 10]: atom OW Res SOL-1 has mass 0 ERROR2 [file "topol.top", line 10]: atomHW1 Res SOL-1 has mass 0 ERROR3 [file "topol.top", line 10]: atomHW2 Res SOL-1 has mass 0 In fact, the mass for all above atoms were all defined in atp file. How can i fix it? Thanks a lot. The build steps are follows: 1.Named the atom type in new tip5p.itp. Add them to ffG53a6.atp and ffG53a6nb.itp. In tip5p.itp: [ atoms ]; id at type res nr residu name at name cg nr charge1 5p_O 1 SOL OW 1 02 5p_H 1 SOL HW1 1 0.2413 5p_H 1 SOL HW2 1 0.2414 5p_L 1 SOL OL1 1 -0.2415 5p_L 1 SOL OL2 1 -0.241 In ffG53a6.atp 5p_O 15.99940 ; O TIP5P Water5p_H 1.00800 ; H TIP5P Water5p_L 0.0 ; L TIP5P Water In ffG53a6nb.itp 5p_O 80.000 0.000 A 2.470013e-03 2.278383e-065p_H 10.000 0.000 A 0 05p_L 00.000 0.000 D 0 0 2. Write top file. #include "ffG53a6.itp"#include "tip5p_.itp" [ system ]; NameProtein [ molecules ]; Compound #molsSOL 1 3. Built gro 5 1SOL OW 1 0.321 1.614 0.603 1SOL HW1 2 0.377 1.643 0.675 1SOL HW2 3 0.258 1.555 0.645 1SOL OL1 4 0.358 1.581 0.554 1SOL OL2 5 0.288 1.669 0.574 0.5 0.5 0.54. grompp -f em.mdp Then the errors came. *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Tip5p with gromos 96, error atom has mass 0
主月 ：） wrote: Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file, three errors came even the system just have one tip5p water. The error is : ERROR 1 [file topol.top, line 10]: atom OW Res SOL-1 has mass 0 ERROR 2 [file topol.top, line 10]: atom HW1 Res SOL-1 has mass 0 ERROR 3 [file topol.top, line 10]: atom HW2 Res SOL-1 has mass 0 In fact, the mass for all above atoms were all defined in atp file. How can i fix it? Thanks a lot. The build steps are follows: 1. Named the atom type in new tip5p.itp. Add them to ffG53a6.atp and ffG53a6nb.itp. In tip5p.itp: [ atoms ] ; idat type res nr residu name at name cg nr charge 1 5p_O 1 SOL OW 1 0 2 5p_H 1 SOL HW1 1 0.241 3 5p_H 1 SOL HW2 1 0.241 4 5p_L 1 SOL OL1 1 -0.241 5 5p_L 1 SOL OL2 1 -0.241 In ffG53a6.atp 5p_O 15.99940 ; O TIP5P Water 5p_H 1.00800 ; H TIP5P Water 5p_L 0.0 ; L TIP5P Water In ffG53a6nb.itp 5p_O8 0.000 0.000 A 2.470013e-03 2.278383e-06 5p_H1 0.000 0.000 A 0 0 5p_L0 0.000 0.000 D 0 0 2. Write top file. #include ffG53a6.itp #include tip5p_.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols SOL 1 3. Built gro 5 1SOL OW1 0.321 1.614 0.603 1SOLHW12 0.377 1.643 0.675 1SOLHW23 0.258 1.555 0.645 1SOLOL14 0.358 1.581 0.554 1SOLOL25 0.288 1.669 0.574 0.5 0.5 0.5 4. grompp -f em.mdp Then the errors came. * Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ，82618423 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php put the mass in your tip5p.itp file. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] analyses of g_hbond
Hi, has someone written a script for analyses output of g_hbond. I'm searching for a tool which calculates ratio of hbond to analysis time, and also converts atom nr to atom names. I know only some lines in perl, but if someone has done it, some work has been saved. Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] amber ff and cpp error message
On Monday 04 September 2006 11:40, Florian Haberl wrote: Hi, i got a strange behaviour of amberff implementation in gromacs (http://folding.stanford.edu/ffamber/): cpp is not running without problems or warnings: is in faq as e.sorin mailed me http://folding.stanford.edu/ffamber/FAQ.html#grompp checking input for internal consistency... calling /lib/cpp... In file included from /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03.itp:19, from topol.top:11: /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:538:22: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:540:22: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:541:22: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:544:21: warning: missing whitespace after the macro name /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:555:19: warning: missing whitespace after the macro name processing topology... This are the lines from the error or warning message, i would say *, ' produces them. ; missing nucleic torsions #define proper_X_CT_N*_X 0.0 0.0 0.0 0.0 0.0 0.0 #define proper_X_CM_CT_X 0.0 0.0 0.0 0.0 0.0 0.0 #define proper_X_CK_N*_X 14.22560 0.0 -14.22560 0.0 0.0 0.0 #define proper_X_CB_N*_X 13.80720 0.0 -13.80720 0.0 0.0 0.0 #define proper_X_CA_NC_X 40.16640 0.0 -40.16640 0.0 0.0 0.0 #define proper_X_CQ_NC_X 56.90240 0.0 -56.90240 0.0 0.0 0.0 is this a normal behaviour? OS is suse 10.1 running on x86_64 cpp -v Using built-in specs. Target: x86_64-suse-linux Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp --disable-libssp --enable-java-awt=gtk --enable-gtk-cairo --disable-libjava-multilib --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux Thread model: posix gcc version 4.1.0 (SUSE Linux) /usr/lib64/gcc/x86_64-suse-linux/4.1.0/cc1 -E -quiet -v - -mtune=generic #include ... search starts here: #include ... search starts here: /usr/local/include /usr/lib64/gcc/x86_64-suse-linux/4.1.0/include /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/includ e /usr/include End of search list Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about angle constraints
Hi David,I think maybe the virtual site is suitable for NO3-. But how about PF6-? Please see the .itp file for the PF6-, which is wroten by myself.1. Because all the bond-length are constrainted, there is no energy term in the .itp file. Therefore it is not a problem of energy term, I think. 2. Except the bond-length, the angles F-P-F should be constrainted to be 90 or 180.*** .itp file*[ moleculetype ]; Name PF6- PFN 3[ atoms ]; nr type resnr resid atom cgnr charge mass 1 opls_977 1 PFN PAA 1 1.34 30.97376 2 opls_978 1 PFN FAA1 1 -0.39 18.99840 3 opls_978 1 PFN FAA2 1 -0.39 18.99840 4 opls_978 1 PFN FAA3 1 - 0.39 18.99840 5 opls_978 1 PFN FAA4 1 -0.39 18.99840 6 opls_978 1 PFN FAA5 1 -0.39 18.99840 7 opls_978 1 PFN FAA6 1 -0.39 18.99840[ constraints ] 1 2 1 0.1560 1 3 1 0.1560 1 4 1 0.1560 1 5 1 0.1560 1 6 1 0.1560 1 7 1 0.1560; The structure of PF6- is Octahedral[ constraints ] 2 3 2 0.2206 2 4 2 0.2206 2 5 2 0.3120 2 6 2 0.2206 2 7 2 0.2206 3 4 2 0.2206 3 5 2 0.2206 3 6 2 0.3120 3 7 2 0.2206 4 5 2 0.2206 4 6 2 0.2206 4 7 2 0.3120 5 6 2 0.2206 5 7 2 0.2206 6 7 2 0.2206 *** .top file** ;the force field files to be included#include ffoplsaa.itp; include the PF6- topology#include PFN.itp[ system ]PFN[ molecules ]; molecule name number PFN 52006/8/30, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Hi All, In my simulation, the NO3- is used, in which the three N-O bond length is constraints. And a planar triangular structure is used. I used the type 1 of [ constraints ] to constraint the bond length. Because I only find angle constraints which is used on H-involved angles, I used the type 2 of [ constraints ] to constraint the length between Os.(The distance is calculated from the triangular structure). After the Energy Minimization, all the bong length become very long (much bigger than the box length). Who knows how to solve it?You probably have an error in the topology. Check energy terms.However, you probably should consider modeling this using either an improper dihedral to keep the N in the plane or, if you want to keep themolecule planar at every time use a virtual site representation for the N. Sincerely yours, Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Swedenphone:46 18 471 4205fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about angle constraints
Qiao Baofu wrote: Hi David, I think maybe the virtual site is suitable for NO3-. But how about PF6-? Please see the .itp file for the PF6-, which is wroten by myself. 1. Because all the bond-length are constrainted, there is no energy term in the .itp file. Therefore it is not a problem of energy term, I think. 2. Except the bond-length, the angles F-P-F should be constrainted to be 90 or 180. this may work, just try it. However, be careful that the number of degrees of freedom is correct, that is it won't be correct! You will have to adapt the temperature in your simulation to match it. *** .itp file* [ moleculetype ] ; Name PF6- PFN 3 [ atoms ] ; nrtyperesnr resid atom cgnr chargemass 1opls_977 1PFNPAA11.34 30.97376 2opls_978 1PFN FAA11 -0.39 18.99840 3opls_978 1PFN FAA21 -0.39 18.99840 4opls_978 1PFN FAA31 - 0.39 18.99840 Typo on the above line... 5opls_978 1PFN FAA41 -0.39 18.99840 6opls_978 1PFN FAA51 -0.39 18.99840 7opls_978 1PFN FAA61 -0.39 18.99840 [ constraints ] 1 21 0.1560 1 31 0.1560 1 41 0.1560 1 51 0.1560 1 61 0.1560 1 71 0.1560 ; The structure of PF6- is Octahedral [ constraints ] 2 32 0.2206 2 42 0.2206 2 52 0.3120 2 62 0.2206 2 72 0.2206 3 42 0.2206 3 52 0.2206 3 62 0.3120 3 72 0.2206 4 52 0.2206 4 62 0.2206 4 72 0.3120 5 62 0.2206 5 72 0.2206 6 72 0.2206 *** .top file** ;the force field files to be included #include ffoplsaa.itp ; include the PF6- topology #include PFN.itp [ system ] PFN [ molecules ] ; molecule name number PFN 5 2006/8/30, David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Qiao Baofu wrote: Hi All, In my simulation, the NO3- is used, in which the three N-O bond length is constraints. And a planar triangular structure is used. I used the type 1 of [ constraints ] to constraint the bond length. Because I only find angle constraints which is used on H-involved angles, I used the type 2 of [ constraints ] to constraint the length between Os. (The distance is calculated from the triangular structure). After the Energy Minimization, all the bong length become very long (much bigger than the box length). Who knows how to solve it? You probably have an error in the topology. Check energy terms. However, you probably should consider modeling this using either an improper dihedral to keep the N in the plane or, if you want to keep the molecule planar at every time use a virtual site representation for the N. Sincerely yours, Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the
[gmx-users] AFM pull and ensembles
Hi all,I have two questions about PMF calculations. 1) Which one is more suggested for an AFM pull simulation, an NVT or an NPT ensemble? I am trying both vacuo and solvated runs (with OPLS-AA ff). 2) My second question is about solvation: I found out that pulling action is much smoother in solvent than in vacuo. It may be bad to have energy and rms jumps in vacuo. On the other hand, I think it would be betterforestimating forces and energy differences with an abrupt change in the system. What is you opinion about effects of solvation?Thanks in advanceMurat Cetinkaya___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RB-dihedral replacing 1-4 interactions
Bond rotations in the carbon tails were modeled with Ryckaert-Bellemans dihedrals and the corresponding 1,4 interactions removed (Lindahl and Edholm, Biophys J., 79, 426-433) When doing a parameter substitution in this way, exactly what 1,4 interactions should be removed? I am using the pope.itp file from Dr. Tieleman's website and my specific question is why, when the double bond is atom 24 to atom 25, does the [pairs] group contain 22-25 and 24-27, but there are no defined [pairs] for 21-24 or 25-28? The general structure around the double bond looks like this: 21 LP2 22 LP2 23 LP2 24 LH1 || double bond 25 LH1 26 LP2 27 LP2 28 LP2 Below I have extracted any reference to atoms 21 to 28 from pope.itp: [ atoms ] 21LP21 POPE C21 7 014.0270 ; qtot: 22LP21 POPE C22 8 014.0270 ; qtot: 23LP21 POPE C23 9 014.0270 ; qtot: 24LH11 POPE C24 10 013.0190 ; qtot: 25LH11 POPE C25 11 013.0190 ; qtot: 26LP21 POPE C26 12 014.0270 ; qtot: 27LP21 POPE C27 13 014.0270 ; qtot: 28LP21 POPE C28 14 014.0270 ; qtot: [ bonds ] 2122 1 0.15300E+00 0.33470E+06 2223 1 0.15300E+00 0.33470E+06 2324 1 0.15300E+00 0.33470E+06 2425 1 0.13900E+00 0.41840E+06 ; double bond 2526 1 0.15300E+00 0.33470E+06 2627 1 0.15300E+00 0.33470E+06 2728 1 0.15300E+00 0.33470E+06 [ pairs ] 2225 1; pair around double bond 2427 1; pair around double bond [ angles ] 212223 1 0.11100E+03 0.46020E+03 222324 1 0.11100E+03 0.46020E+03 232425 1 120.000 502.080 ; cis thingies 242526 1 120.000 502.080 ; cis thingies 252627 1 0.11100E+03 0.46020E+03 262728 1 0.11100E+03 0.46020E+03 [dihedrals] 21222324 3 22232425 1 0.000 5.858 3 23242526 2 0.000 167.360 24252627 1 0.000 5.858 3 25262728 3 Thanks for any assistance, Chris Neale. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
