Re: [gmx-users] the dipole correlation function of SPC/E water
Tanping Li wrote: Dear all, I simulated a box of pure water usin NPT. I use gmx96 force field and standard mdp file for the gmx96 force field. The time scale of dipole correlation function is 2.8ps, which is different from David's result 3.8ps in the JCP paper. Is this 3.8ps sensitive to the mdp file or the force field? I just wonder if there is a bug in my program. I tried a lot, but still can't get 3.8ps. Really appretiate your idea, I have struggled for this for a long time. You need to use *exactly* the same parameters to reproduce it, in particular cutoffs and reaction field, dispersion correction and so on. Yours Tanping ___ 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, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compile problem
Florian Haberl wrote: hi On Thursday 06 April 2006 09:24, Rongliang Wu wrote: make: warning: Clock skew detected. Your build may be incomplete make is using the latest modified time stamps on each file to see if it needs recompiling. If you have changed your date latly or it was wrong than it is in the future and make will complain. ... or if the machine serving a network file structure has a time different from the machine you're running on. I have some intransigent clock-slowing SGIs that ntpd just won't work properly on... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx(ver3.3) contain bug?
Hi I'm going to simulate a HEME-Protein complex using GROMACS 3.3, and try pdb2gmx -f pdb1a6n.ent and select 0: GROMOS96 43a1 force field But, pdb2gmx cannot link FE(HEME) to NE2(HIS). pdb2gmx outputs Opening library file /home/kameda/gromacs-3.3/share/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: HEME152 HEME152 FE1204 CAB1226 HEME152 CAB1226 0.565 HEME152 CAC1234 0.569 0.800 ? On trial, I type same command using version3.2.1, then output is Opening library file /usr/local/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: HIS12 HIS24 HIS36 HIS48 HIS64 HIS64 HIS81 NE2109 NE2199 NE2311 NE2430 NE2577 NE2578 NE2697 HIS24 NE2199 1.250 HIS36 NE2311 2.726 1.886 HIS48 NE2430 3.627 2.393 2.106 HIS64 NE2577 2.764 1.756 1.685 1.412 HIS64 NE2578 2.698 1.666 1.546 1.376 0.151 HIS81 NE2697 2.219 2.576 3.044 4.059 2.682 2.694 HIS82 NE2707 2.294 2.194 2.241 3.274 1.902 1.905 0.931 HIS93 NE2797 2.824 2.010 1.628 1.927 0.622 0.653 2.312 HIS97 NE2833 3.213 2.349 1.977 1.830 0.689 0.789 2.620 HIS113 NE2973 2.044 1.304 1.082 2.451 2.139 1.994 3.153 HIS116 NE21007 1.571 1.352 1.669 3.117 2.612 2.481 2.958 HIS116 NE21008 1.389 1.285 1.790 3.192 2.630 2.505 2.849 HIS119 NE21044 1.015 0.267 1.997 2.650 1.994 1.904 2.543 HEME152 FE1337 2.722 1.843 1.539 1.764 0.440 0.449 2.388 HEME152 CAB1359 2.255 1.512 1.325 2.115 0.865 0.806 2.024 HEME152 CAC1367 2.930 1.969 1.108 1.581 0.740 0.656 2.769 HIS82 HIS93 HIS97 HIS113 HIS116 HIS116 HIS119 NE2707 NE2797 NE2833 NE2973 NE21007 NE21008 NE21044 HIS93 NE2797 1.448 HIS97 NE2833 1.794 0.468 HIS113 NE2973 2.576 2.261 2.646 HIS116 NE21007 2.583 2.666 3.095 0.748 HIS116 NE21008 2.524 2.681 3.113 0.893 0.190 HIS119 NE21044 2.235 2.203 2.564 1.318 1.217 1.121 HEME152 FE1337 1.545 0.214 0.555 2.115 2.541 2.558 2.048 HEME152 CAB1359 1.199 0.626 1.082 1.760 2.076 2.078 1.668 HEME152 CAC1367 1.878 0.650 0.887 1.881 2.421 2.480 2.169 HEME152 HEME152 FE1337 CAB1359 HEME152 CAB1359 0.565 HEME152 CAC1367 0.569 0.800 Linking HIS-93 NE2-797 and HEME-152 FE-1337... and .top file shows the linkage, for example, [atoms] 926 NR 93 HIS1NE2388 -0.5814.0067 ; qtot 1 1521FE152 HEME FE6430.4 55.847 ; qtot 2.4 ... [bonds] ... 926 1521 2 The line '926 1521 2' does not exist in .top file made by GROMACS 3.3. For your information, there are not difference between /home/kameda/gromacs-3.3/share/top/specbond.dat with /usr/local/share/gromacs/top/specbond.dat. Is it caused by Bug ?? Thanks Tomoshi Kameda ___ 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
R: [gmx-users] Gromacs 3.3 manual
Dear Stéphane I am interested in a PDF format of the manual for Gromacs 3.3. Let me know if you can send it to me. Best regards Andrea Andrea Stevenazzi Medicinal Computer Chemistry Italfarmaco Research Centre Italfarmaco SpA Via dei Lavoratori 54 20092 Cinisello Balsamo Milan E-mail: [EMAIL PROTECTED] Tel: +39-02-64433097 -Messaggio originale- Da: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Per conto di Stéphane Teletchéa Inviato: lunedì 20 marzo 2006 11.59 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] Gromacs 3.3 manual Andrea Carotti a écrit : Thank you for the fast answer. Please let me (us) know, when it will be fixed. Thanks Andrea I did a cvs manual as of february 2nd, 2006. If you are interested in the PDF, let me know, i'll send you. Regards, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] diheadral PCA method
Dear All, Some of you want comments on the dihedral PCA analysis. Here I give the link to one comment on that which will appear in Proteins although we do not agree with their main result. Also you can find our reply to that comment. http://www.ntu.edu.sg/home/ygmu Best regards Yuguang Dr. Yuguang Mu Assistant Professor Division of Structural and Computational Biology School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: 63162885 Fax: 67913856 ___ 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] pbc doubt
Hi all, I have a doubt with the pbc applied in the MD. I converted the xtc file in pdb with trjconv. Checking with rasmol the pdb file, I found that the protein is always not broke in fragments and the box is always fix. Subsequently, I tried to use the option -pbc whole, which breaks the protein in more fragments, but the box is always fix, not spanned. I would like to analyze my gromacs trajectory making some codes written from my self, but I have this pbc doubt. So, how can I remove the pbc from the xtc files? I think that for the protein in the xtc file pbc are already removed, but for the solvent are not removed. Let me to ask another question: Do you think that for the trajectory analysis with my fortran codes I can use the format g96? Thanks in advance, cheers, Adriana -- _ Adriana Pietropaolo, PhD student, dipartimento di Chimica Fisica ed Inorganica, Facolta' di Chimica Industriale Universita' di Bologna WEB:www2.fci.unibo.it/~adriana Tel 051/6446992 FAX 051/2093690 _ ___ 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] the dipole correlation function of SPC/E water
Tanping Li wrote: Dear David, Thank you so much for the reply. I used the pme, cutoff for rvdw =1.4, rlist=rcoulomb=0.9, so that is not supposed to give me the same rotational relaxation time for SPC/E as 3.8ps in your paper? No. If you want to reproduce literature you have to do it exactly the same way. Best Tanping --- David van der Spoel [EMAIL PROTECTED] wrote: Tanping Li wrote: Dear all, I simulated a box of pure water usin NPT. I use gmx96 force field and standard mdp file for the gmx96 force field. The time scale of dipole correlation function is 2.8ps, which is different from David's result 3.8ps in the JCP paper. Is this 3.8ps sensitive to the mdp file or the force field? I just wonder if there is a bug in my program. I tried a lot, but still can't get 3.8ps. Really appretiate your idea, I have struggled for this for a long time. You need to use *exactly* the same parameters to reproduce it, in particular cutoffs and reaction field, dispersion correction and so on. Yours Tanping ___ 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, 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 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, 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] boundary conditions
Hi, I've a DNA molecule, and I want to simulate MD when the DNA has an extremity fixed. So I have to block some degree of freedom. How could I do this? thanks Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3___ 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] Re: structure factor
Hi Warren and gmx'users,
I tried what Warren ask me in the last e-mail and I still had some problems. Look this ---
I read your answer about my ask 'structure factor' and I did what you
wrote, but the g_rdf searching a list and return the message:
##
Fatal error:
Error: atom type (opls_557) not in list (18 types checked)!
#
In the font program of gmx_rdf.c have:
#
int return_atom_type (char *type)
{
int i;
for (i = 0; (i asize(CM_t)); i++)
if (!strcmp (type, CM_t[i].Label))
return i;
gmx_fatal(FARGS,\nError: atom type (%s) not in list (%d types checked)!\n,
type,i);
return 0;
}
#
I think that it search a string that correspond to atom type in
opls_XXX. When I had construct my input file and how the system wasn't
protein or biomolecules, being polymers, I setted new opls_XXX.
Why would be this list ?!?!? It would be a table with default atom type
of gromacs ?!?! What should I do in this case, because the MD
simulations are ok !!
thanks --
Message: 9Date: Thu, 06 Apr 2006 10:13:53 +1000From: Dallas B. Warren [EMAIL PROTECTED]Subject: RE: [gmx-users] structural factor with g_rdf
To: Discussion list for GROMACS users gmx-users@gromacs.orgMessage-ID:
[EMAIL PROTECTED]Content-Type: text/plain; charset=US-ASCIII think you may find it is referring to a .tpr file.So use the -s switch, with the .tpr file that is associated with the
trajectory file you are analysing.Catch ya,Dr. Dallas WarrenLecturerDepartment of Pharmaceutical Biology and PharmacologyVictorian College of Pharmacy, Monash University381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]+61 3 9903 9524-When the only tool you own is a hammer, every problem begins to resemble
a nail.--___gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-usersEnd of gmx-users Digest, Vol 24, Issue 16*-- ### Luciano Tavares da Costa ###
## MSc. Eng. Químico## 100 % Linux#
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[gmx-users] FEP and position restraints
Hi allIm doing FEP calculation on Zn ions.Is three a way to put position restraints on perturbated / dummy atoms.When I define in my system.top: #include "zn.itp"[ position_restraints ]; i funct fcx fcy fcz 1 1 1000 1000 1000 #include "cl.itp"[ position_restraints ]; i funct fcx fcy fcz 1 1 1000 1000 1000 #include "dum.itp"[ position_restraints ]; i funct fcx fcy fcz 1 1 1000 1000 1000 [ system ].. .. Im perturbating Zn ions into dummy atoms. (Im using ffgmx Ive added new DUM atomtype)When I use grompp I get following warning: checking input for internal consistency...calling /lib/cpp...processing topology...Generated 1238 of the 2080 non-bonded parameter combinationsWARNING 1 [file "system.top", line 11]: No default Position Rest. types for perturbed atoms, using normal valuesWARNING 2 [file "system.top", line 21]: No default Position Rest. types for perturbed atoms, using normal valuesExcluding 3 bonded neighbours for Protein 1turning H bonds into constraints... How can I apply position restraints on them. Please give me some comment on this and thank you in advance!!All best. ___ 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] seperating bilayers (again)
Hello all, I've been having some trouble recently with the leaflets in my bilayer gently drifting apart over a period of a few hundred picoseconds. Increasing the vdW radius hasn't helped (up to 2nm), although it did delay the seperation. Likewise, increasing tau_p from 5 up to 10. The really bizarre thing is that I've been simulating peptides in bilayers using 3.2.1 on our cluster for about 18 months now, using the lipid-modified version of ffgmx and the parameters listed below, and it's only since I've started using 3.3 on a new machine that I've had any trouble. Any suggestions on what might be going wrong? title = Yo cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.0015 ; ps ! nsteps = 500 ; total 7500 ps. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid coulombtype = PME rlist = 1.5 rcoulomb= 1.5 rvdw= 1.5 pme_order = 8 fourierspacing = 0.2 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = DOPC SOL Protein Cl tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 ; Energy monitoring energygrps = DOPC SOL Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = surface-tension tau_p = 5 compressibility = 4.5e-5 4.5e-5 ref_p = 410 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] FEP and position restraints
Right. Thank you for help. Now it works fine. :) - Original Message - From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Thursday, April 06, 2006 6:02 PM Subject: RE: [gmx-users] FEP and position restraints From: P [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] FEP and position restraints Date: Thu, 6 Apr 2006 17:52:10 +0200 Hi all I'm doing FEP calculation on Zn ions. Is three a way to put position restraints on perturbated / dummy atoms. When I define in my system.top: . . #include zn.itp [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #include cl.itp [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #include dum.itp [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 [ system ] .. . .. I'm perturbating Zn ions into dummy atoms. (I'm using ffgmx I've added new DUM atomtype) When I use grompp I get following warning: .. .. checking input for internal consistency... calling /lib/cpp... processing topology... Generated 1238 of the 2080 non-bonded parameter combinations WARNING 1 [file system.top, line 11]: No default Position Rest. types for perturbed atoms, using normal values WARNING 2 [file system.top, line 21]: No default Position Rest. types for perturbed atoms, using normal values Excluding 3 bonded neighbours for Protein 1 turning H bonds into constraints... .. .. How can I apply position restraints on them. Please give me some comment on this and thank you in advance!! All best. You have already done it. But as you are doing a free energy calculation, grompp expect also 3 force constants for the B topology. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] missing residues
Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Please suggest suggestions on how? I go about building these missing residues and integrating with the crystallographically resolved structure such that I can proceed with MD simulations. Thanks Jayant Jayasundar JayantJames Postdoctoral researchfellow, Department ofVeterinary andComparative Anatomy,Pharmacology andPhysiology(VCAPP), Washingtonstate university,Pullman 99164-6520,USA. http://www.chick.com/reading/tracts/0001/0001_01.asp ___ 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] missing residues
Quoting Jayant James Jayasundar [EMAIL PROTECTED]: Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Hi Are those residues in the Nter/Cter ? If they are, perhaps leaving the protein without them would be my first approach. The decision could pass by knowing what's the biological relevance of those residues on the whole protein structure. If they are not terminal residues, then you could try to add them with a molecular modeling program like (though 17 residues is a big chunk): swisspdb viewer, jackal, PLOP ... Best regards, Nuno Please suggest suggestions on how? I go about building these missing residues and integrating with the crystallographically resolved structure such that I can proceed with MD simulations. Thanks Jayant Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp This message was sent using IMP, the Internet Messaging Program. ___ 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] missing residues
At 06:25 PM 4/6/2006 +, you wrote: Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Please suggest suggestions on how? I go about building these missing residues and integrating with the crystallographically resolved structure such that I can proceed with MD simulations. Thanks Jayant Swiss PDB viewer can do this, including optimizing the side chain positions. http://us.expasy.org/spdbv/ Jayasundar Jayant James Postdoctoral research fellow, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]f990e0db.jpg ___ 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 Professor Ray Fort Jr. [EMAIL PROTECTED] Department of Chemistry chemistry.umeche.maine.edu/fort.html University of Maine Voice: (207)-581-1180 Orono, ME 04469 FAX: (207)-581-1191 Computer modeling of organic and biomolecules; chemistry of lignin and celluloseattachment: f990e0db.jpg ___ 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] Handling protein chain breaks
Hi. I am running dynamics with the protein trypsin. It turns out that it has 2 aminoacids missing in the middle of the chain. pdb2gmx is making a peptide bond between aminoacid i and i+3. Which is the best way to go: 1. Give separate names for the chains before and after the break. 2. Just comment out the lines in the top file where the atoms involved in this bond appear. 3. Other options??? Thanks, joao. ___ 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] seperating bilayers (again)
Alan Dodd wrote: Hello all, I've been having some trouble recently with the leaflets in my bilayer gently drifting apart over a period of a few hundred picoseconds. Increasing the vdW radius hasn't helped (up to 2nm), although it did delay the seperation. Likewise, increasing tau_p from 5 up to 10. The really bizarre thing is that I've been simulating peptides in bilayers using 3.2.1 on our cluster for about 18 months now, using the lipid-modified version of ffgmx and the parameters listed below, and it's only since I've started using 3.3 on a new machine that I've had any trouble. Any suggestions on what might be going wrong? pme_order = 8 pme_order != 4 is known to be buggy in the distribution version of 3.3 - see multiple mailing list threads. There is a fixed pme.c on the ftp site that you can find somewhere on the gromacs webpage. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PCA eigenvalue normalization
Have you checked if your peptide is jumping out of the box? Regards. Pedro Hello, I have performed PCA analysis, without mass weighting, on a peptide using g_covar and g_anaeig. The first principal component generally corresponds to the stretching of the peptide. I understand that each eigenvalue represents the variance in the motion along the associated eigenvector. However, the square root of the variance for the first eigenvalue is ~20 nm while the maximum extended length of any peptide is ~3 nm. I have tried normalizing the eigenvalues by the number of atoms used for the analysis (73) but this gives the standard deviation of the motion to be ~2.2 nm, still much too large. I would like to know how to normalize the eigenvalues to obtain reasonable standard deviations from the eigenvalues. Thank you, Tyler This message was sent using IMP, the Internet Messaging Program. ___ 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] Gromacs 3.3.1 released
Erik Lindahl wrote: Hi everybody, I'm happy to announce that we've finally gotten version 3.3.1 out - I've just finished uploading source and an assortment of binaries to the website. According to David he also fixed the 3.3 manual, so with a bit of luck we'll see that online too in a day or two. Great work! All bugs that were in bugzilla as of March 31 have been fixed. You can find a live list of all current reports at http:// bugzilla.gromacs.org/buglist.cgi?product=Gromacsversion=3.3 The archive of the gmx-revision list ( http://www.gromacs.org/ pipermail/gmx-revision/ ) also contains a number of improvements, for instance that we now support SSE assembly loops on Intel Macs too. Is there a bugfix list also? Neither of the above appears to document the resolution of the evergreen 3.3 pme_order != 4 problem. Doubtless there are other things people care about too... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] seperating bilayers (again)
pme.c has already been patched - I've been caught out on that previously. I tried pme_order=4 anyway, just in case - it didn't help. --- Mark Abraham [EMAIL PROTECTED] wrote: Alan Dodd wrote: Hello all, I've been having some trouble recently with the leaflets in my bilayer gently drifting apart over a period of a few hundred picoseconds. Increasing the vdW radius hasn't helped (up to 2nm), although it did delay the seperation. Likewise, increasing tau_p from 5 up to 10. The really bizarre thing is that I've been simulating peptides in bilayers using 3.2.1 on our cluster for about 18 months now, using the lipid-modified version of ffgmx and the parameters listed below, and it's only since I've started using 3.3 on a new machine that I've had any trouble. Any suggestions on what might be going wrong? pme_order = 8 pme_order != 4 is known to be buggy in the distribution version of 3.3 - see multiple mailing list threads. There is a fixed pme.c on the ftp site that you can find somewhere on the gromacs webpage. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] Gromacs 3.3.1 released
Hi Mark, On Apr 7, 2006, at 12:12 AM, Mark Abraham wrote: Is there a bugfix list also? Neither of the above appears to document the resolution of the evergreen 3.3 pme_order != 4 problem. Doubtless there are other things people care about too... I think the PME issue was fixed by David before anybody reported it, and thus it never showed up in bugzilla. We're changing this now, and try to add all bugs there even if we immediately fix them ourselves. A bug list is in progress in the form of a gmx-commit list (and possibly web page) that will archive every single CVS commit command automatically. Cheers, Erik ___ 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] Manual 3.3 and online docs ready too...
Hi, I was on a flow tonight, so I found some time to build the manual and online docs to - you can find them on the website! Cheers, Erik ___ 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] Re: PCA eigenvalue normalization
Hello, Thank you for the previous responses. I still have some questions about the eigenvalues however. I should note that the frames of my trajectory have been fit to a reference structure using the backbone atoms of the first three residues. This is because the peptide is a fragment of a much larger protein. 1) If I wish to compare the eigenvalues of several peptides of different lengths how would I normalize the eigenvalues? Do I simply divide by the number of atoms used in the calculation? 2) If the eigenvalue represents the sum of the variances for each particle along the eigenvector then dividing the eigenvector by the number of atoms used in the calculation should be the average variance. Likewise, the square root of this should be the average standard deviation per atom. In my case, the first eigenvector is a stretching in the length of the peptide. Shouldn't the average standard deviation per atom along this stretching motion be smaller that the standard deviation in the length of the entire peptide, or at least smaller than the extended length of the peptide? Thank you, Tyler Hi Tyler, Note that the eigenvalue represents the sum of the variances for each particle along the associated eigenvector. That seems quite reasonable to me. Tsjerk On 4/6/06, Tyler Luchko [EMAIL PROTECTED] wrote: Hello, I have performed PCA analysis, without mass weighting, on a peptide using g_covar and g_anaeig. The first principal component generally corresponds to the stretching of the peptide. I understand that each eigenvalue represents the variance in the motion along the associated eigenvector. However, the square root of the variance for the first eigenvalue is ~20 nm while the maximum extended length of any peptide is ~3 nm. I have tried normalizing the eigenvalues by the number of atoms used for the analysis (73) but this gives the standard deviation of the motion to be ~2.2 nm, still much too large. I would like to know how to normalize the eigenvalues to obtain reasonable standard deviations from the eigenvalues. Thank you, Tyler (_Tyler Luchko Ph.D. Candidate_) _) Department of PhysicsUniversity of Alberta (_ (_Edmonton, Alberta, Canada _) _) 780-492-1063 [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 -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/ 20060406/0ffa9560/attachment-0001.html ___ 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] boundary conditions
Use position constraints? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] grompp error
Hello, gmx-users， i met with this error when using the grompp command in gromacs-3.3.1, which went well with gromacs-3.3: Tried to execute: '/usr/bin/cpp -I/export/home/wurl/software/gromacs/share/top ao7.top grompp1LQeAz' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... Cleaning up temporary file grompp1LQeAz --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file ao7.top, line 13 --- and top file is as follows: ; ; File 'ao7.top' was generated ; By user: wurl (1006) ; On host: IBMWU ; At date: Wed Apr 5 17:17:00 2006 ; ; This is your topology file ; GROningen MAchine for Chemical Simulation ; ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_135 1AO7 CA 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1AO7HA1 1 0.06 1.008 ; qtot -0.12 3 opls_140 1AO7HA2 1 0.06 1.008 ; qtot -0.06 4 opls_140 1AO7HA3 1 0.06 1.008 ; qtot 0 5 opls_136 1AO7 CB 2 -0.12 12.011 ; qtot -0.12 6 opls_140 1AO7HB1 2 0.06 1.008 ; qtot -0.06 7 opls_140 1AO7HB2 2 0.06 1.008 ; qtot 0 8 opls_136 1AO7 CC 3 -0.12 12.011 ; qtot -0.12 9 opls_140 1AO7HC1 3 0.06 1.008 ; qtot -0.06 10 opls_140 1AO7HC2 3 0.06 1.008 ; qtot 0 11 opls_136 1AO7 CD 4 -0.12 12.011 ; qtot -0.12 12 opls_140 1AO7HD1 4 0.06 1.008 ; qtot -0.06 13 opls_140 1AO7HD2 4 0.06 1.008 ; qtot 0 14 opls_136 1AO7 CE 5 -0.12 12.011 ; qtot -0.12 15 opls_140 1AO7HE1 5 0.06 1.008 ; qtot -0.06 16 opls_140 1AO7HE2 5 0.06 1.008 ; qtot 0 17 opls_136 1AO7 CF 6 -0.12 12.011 ; qtot -0.12 18 opls_140 1AO7HF1 6 0.06 1.008 ; qtot -0.06 19 opls_140 1AO7HF2 6 0.06 1.008 ; qtot 0 20 opls_136 1AO7 CG 7 -0.12 12.011 ; qtot -0.12 21 opls_140 1AO7HG1 7 0.06 1.008 ; qtot -0.06 22 opls_140 1AO7HG2 7 0.06 1.008 ; qtot 0 23 opls_136 1AO7 CH 8 -0.12 12.011 ; qtot -0.12 24 opls_140 1AO7HH1 8 0.06 1.008 ; qtot -0.06 25 opls_140 1AO7HH2 8 0.06 1.008 ; qtot 0 26 opls_136 1AO7 CI 9 -0.12 12.011 ; qtot -0.12 27 opls_140 1AO7HI1 9 0.06 1.008 ; qtot -0.06 28 opls_140 1AO7HI2 9 0.06 1.008 ; qtot 0 29 opls_136 1AO7 CJ 10 -0.12 12.011 ; qtot -0.12 30 opls_140 1AO7HJ1 10 0.06 1.008 ; qtot -0.06 31 opls_140 1AO7HJ2 10 0.06 1.008 ; qtot 0 32 opls_136 1AO7 CK 11 -0.12 12.011 ; qtot -0.12 33 opls_140 1AO7HK1 11 0.06 1.008 ; qtot -0.06 34 opls_140 1AO7HK2 11 0.06 1.008 ; qtot 0 35 opls_182 1AO7 CL 12 0.14 12.011 ; qtot 0.14 36 opls_185 1AO7HL1 12 0.03 1.008 ; qtot 0.17 37 opls_185 1AO7HL2 12 0.03 1.008 ; qtot 0.2 38 opls_180 1AO7 O1 12 -0.415.9994 ; qtot -0.2 39 opls_182 1AO7 CM 12 0.14 12.011 ; qtot -0.06 40 opls_185 1AO7HM1 12 0.03 1.008 ; qtot -0.03 41 opls_185 1AO7HM2 12 0.03 1.008 ; qtot 0 42 opls_182 1AO7 CN 13 0.14 12.011 ; qtot 0.14 43 opls_185 1AO7HN1 13 0.03 1.008 ; qtot 0.17 44 opls_185 1AO7HN2 13 0.03 1.008 ; qtot 0.2 45 opls_180 1AO7 O2 13 -0.415.9994 ; qtot -0.2 46 opls_182 1AO7 CO 13 0.14 12.011 ; qtot -0.06 47 opls_185 1AO7HO1 13 0.03 1.008 ; qtot -0.03 48 opls_185 1AO7
[gmx-users] Energy constraints and belly dynamics
Dear gromacs users, I have two queries. 1. What are the energy values (in kcal/mol) for the constraints applied during protein simulations? 2. Is there any way to do belly dynamics in gromacs i.e. can we restrain few residues around the ligand and constrain rest of the part ? Thanks Regards, Shankar Prasad Kanaujia Ph.D Student Bioinformatics Center, Department of SERC IISc, Bangalore - 12 Mobile: 9845631581 ___ 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
