[gmx-users] RE: transport properties
Please read about obtaining diffusion constant from VAC in the gromacs wiki. I wrote an individual article on that topic. Best, Vitaly Subject: RE: [gmx-users] transport properties To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 569363.99887...@web36304.mail.mud.yahoo.com Content-Type: text/plain; charset=utf-8 Dear K. Chae, Thank you very much for your answer. I computed velocity auto-correlation (VAC) functions , but how can I integrate velocity auto-correlation (VAC) functions to get Diffusion coefficient using xmgrace software ? I have just used xmgrace to plot md result for analysis. And I have a limited information using xmgrace. Could you please explain the integration procedure in xmgrace ? I will be very grateful if you can help me to learn how to calculate Diffusion coefficient . Thanks in advance for your helps. Best regards, --- On Tue, 4/28/09, kyungchan chae ckcu...@umich.edu wrote: From: kyungchan chae ckcu...@umich.edu Subject: RE: [gmx-users] transport properties To: 'Discussion list for GROMACS users' gmx-users@gromacs.org Date: Tuesday, April 28, 2009, 9:52 AM Once you have correlation results then xmgrace software can do the integration. Regards Dear All, I'm trying to calculate self diffusion coefficient from velocity auto-correlation (VAC) functions using Green-Kubo relation in figure I attached to the mail. I couldn’t solve how to integrate the velocity auto-correlation (VAC) functions to get Diffusion coefficient. Could you please give me some information about this issue ? Could you suggest some software to integrate the VAC function ? Thanks in advance for your helps. Best regards, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] itp for rigid acetone
the parameter of acetone in the literature( JPC 94, 1990, p.1683) are given in the following manner, atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O -0.424 2.960 0.210 ** C=O distance :0.1222 nm CH3-C distance: 0.1507 angles: O=C-CH3:121.44 CH3-C-CH3:117.12 In the model, the bond lengths and bond angles have been kept fixed for all MD simulation of acetone. I have no idea on how to set up the itp file for aceton so that the bond lengths and bond angles have been kept fixed Somebody can help me to give me the case of itp file. -- Xin Liu 2009-04-29 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Dear Justin and Dallas: Thank you for your help earlier. I made a copy of ffoplsaa.rtp to my working directory and add a new residue to it. Then perform the following command: pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 6 Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- And also my pdb file: ATOM 1 Si1 PDM A 1 3.796 2.499 -0.834 1.00 0.00 ATOM 2 O2 PDM A 1 4.661 1.181 -0.025 1.00 0.00 ATOM 3 Si4 PDM A 1 4.896 -0.181 1.082 1.00 0.00 ATOM 4 O6 PDM A 1 3.686 -1.442 0.846 1.00 0.00 ATOM 5 Si7 PDM A 1 2.036 -2.061 0.903 1.00 0.00 ATOM 6 O8 PDM A 1 2.038 -3.727 0.331 1.00 0.00 ATOM 7 Si9 PDM A 1 1.180 -5.229 0.010 1.00 0.00 ATOM 8 O10 PDM A 1 2.299 -6.424 -0.637 1.00 0.00 ATOM 9 Si16 PDM A 1 3.364 -7.030 -1.904 1.00 0.00 ATOM 10 O17 PDM A 1 4.537 -5.799 -2.367 1.00 0.00 ATOM 11 Si18 PDM A 1 5.956 -5.364 -3.320 1.00 0.00 ATOM 12 O22 PDM A 1 6.259 -3.637 -3.183 1.00 0.00 ATOM 13 Si24 PDM A 1 5.682 -1.997 -3.451 1.00 0.00 ATOM 14 O26 PDM A 1 6.879 -0.842 -2.885 1.00 0.00 ATOM 15 Si28 PDM A 1 8.515 -0.209 -2.996 1.00 0.00 ATOM 16 O29 PDM A 1 8.808 0.346 -4.640 1.00 0.00 ATOM 17 Si30 PDM A 1 9.879 1.063 -5.838 1.00 0.00 ATOM 18 C34 PDM A 1 9.731 -1.561 -2.566 1.00 0.00 ATOM 19 C36 PDM A 1 8.720 1.221 -1.809 1.00 0.00 ATOM 20 C38 PDM A 1 6.585 -0.914 0.764 1.00 0.00 ATOM 21 C40 PDM A 1 4.835 0.406 2.852 1.00 0.00 ATOM 22 C42 PDM A 1 5.391 -1.730 -5.278 1.00 0.00 ATOM 23 C44 PDM A 1 4.080 -1.754 -2.529 1.00 0.00 ATOM 24 C46 PDM A 1 7.441 -6.315 -2.701 1.00 0.00 ATOM 25 C48 PDM A 1 5.652 -5.789 -5.115 1.00 0.00 ATOM 26 C50 PDM A 1 2.345 -7.495 -3.401 1.00 0.00 ATOM 27 C52 PDM A 1 4.259 -8.545 -1.272 1.00 0.00 ATOM 28 C54 PDM A 1 0.462 -5.872 1.612 1.00 0.00 ATOM 29 C56 PDM A 1 -0.201 -4.930 -1.214 1.00 0.00 ATOM 30 C58 PDM A 1 1.428 -2.016 2.670 1.00 0.00 ATOM 31 C60 PDM A 1 0.900 -1.032 -0.161 1.00 0.00 ATOM 32 O62 PDM A 1 3.063 3.615 0.320 1.00 0.00 ATOM 33 Si63 PDM A 1 1.897 4.001 1.587 1.00 0.00 ATOM 34 O64 PDM A 1 2.116 5.675 2.077 1.00 0.00 ATOM 35 Si68 PDM A 1 3.148 6.934 2.744 1.00 0.00 ATOM 36 C69 PDM A 1 3.682 6.458 4.471 1.00 0.00 ATOM 37 C72 PDM A 1 5.023 3.440 -1.884 1.00 0.00 ATOM 38 C74 PDM A 1 2.464 1.816 -1.948 1.00 0.00 ATOM 39 C76 PDM A 1 0.164 3.775 0.923 1.00 0.00 ATOM 40 C78 PDM A 1 2.137 2.886 3.063 1.00 0.00 ATOM 41 C80 PDM A 1 2.202 8.545 2.805 1.00 0.00 ATOM 42 Si84 PDM A 1 4.922 7.171 1.466 1.00 0.00 ATOM 43 C84 PDM A 1 8.984 1.182 -7.476 1.00 0.00 ATOM 44 C86 PDM A 1 10.387 2.774 -5.280 1.00 0.00 ATOM 45 C88 PDM A 1 11.401 -0.004 -6.037 1.00 0.00 TER Do you have any idea what I did wrong? It seems the GROMACS doesn't give the wrong line by Fatal error: in .rtp file at line: --- Thank you so much for your help in advance! On Tue, Apr 28, 2009 at 4:38 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear Justin and Dallas: Thank you for your help earlier. I made a copy of ffoplsaa.rtp to my working directory and add a new residue to it. Then perform the following command: pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 6 Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: Well that's weird. You should use the diff utility on ffoplsaa.rtp before and after your modifications and see what that tells you. If you've edited it on a Windows machine, then you may have line-ending issues. If so, use dos2unix on the file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -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 list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Error by pdb2gmx
Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -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 list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] what is meaning of vol 0.95 imb F 1%?
Dear gmx users, If -v was passed on to mdrun, such rows one by one would be printed continuously as follows: vol 0.95 imb F 1% step 1000, will finish Thu Apr 30 15:39:33 Obviously, the words step 1000, will finish Thu Apr 30 15:39:33 mean that the current running step is 1000, the whole run will finish at 15:39:33, on Thuseday, April 30th. But what it is meant by vol 0.95 imb F 1%? Thank you very much for any reply. Best regards,\ xiaowu _ Live Search视频搜索，快速检索视频的利器！ http://www.live.com/?scope=video___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] what is meaning of vol 0.95 imb F 1%?
wuxiao wrote: Dear gmx users, If -v was passed on to mdrun, such rows one by one would be printed continuously as follows: vol 0.95 imb F 1% step 1000, will finish Thu Apr 30 15:39:33 Obviously, the words step 1000, will finish Thu Apr 30 15:39:33 mean that the current running step is 1000, the whole run will finish at 15:39:33, on Thuseday, April 30th. But what it is meant by vol 0.95 imb F 1%? Thank you very much for any reply. This is the verbose output produced under dynamic load balancing and domain decomposition. A quick look at the code didn't make it clear what vol means (it's some kind of DD workload measure, though), and imb F is the load imbalance between different processors in calculating the forces. I guess that if the two values are reasonably close to 1 and 0% respectively, then things are fine. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Questions
Hi Tsjerk: I still have questions here. 1. Although you have explained the differece between HOH, AHOH and BHOH, I do not fully understand. = Can I delete all of atoms, HOH, AHOH and BHOH ? 2. So, in your tutorial, you use united atom algorithm, right? and, pdb2gmx can recognize the united atoms and give them the proper force fields, right? 3. If one want to use the all-atom algorithm, use the command protonate + protein pdb file first to add all missing hydrogens, then, use pdb2gmx to get an all-atom force field parameters, right? 4. In your last email = where did you get the following information? = I re-check the original 1LW9.pdb = I did not get the information by myself. The answer to this question is in the format specification of the PDB file. The A and B are alternative identifiers and indicate that the electron density can be explained by a water molecule that is partially present at two sites. If you look at the occupancy field you'll notice that the corresponding values are less than 1. In fact, if you sum the occupancies for equivalent atoms in for A and B, they will add up to 1. Thank you very much, Lin On 4/28/09, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lin, I bounce this mail to the gromacs user list as the issues are well off to be archived. I have two stupid questions here. Well, that's up to us to decide ;) 1. I want to get the proper structure of lysozyme. From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL) and 2-hydroxethyl disulfide (HED) are removed. http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ Further, I remove the water, such as HOH, AHOH and BHOH. I don't know what is the differece between HOH, AHOH and BHOH. The answer to this question is in the format specification of the PDB file. The A and B are alternative identifiers and indicate that the electron density can be explained by a water molecule that is partially present at two sites. If you look at the occupancy field you'll notice that the corresponding values are less than 1. In fact, if you sum the occupancies for equivalent atoms in for A and B, they will add up to 1. Then, I add all missing H atoms. = made the new pdb file = it is attached. Would you please take a look if the pdb file is corrct? No, I'm not going to do that. Have a look at the structure to see if it is okay and be sure to take into account whether you used a united atom force field or an all atom one. In your tutorial, why don't you add the missing hydrogen atoms? I do (or rather, I let the students do it ;)). It's one of the things pdb2gmx does. Is it unnecessary to add the missing H atoms? Each residue/molecule should have atoms (with coordinates) matching with the description in the force field used. So if hydrogen atoms are missing with respect to the force field, then they have to be added. HETATM 1504 O HOH 445 36.056 19.096 6.798 1.00 34.30 O HETATM 1535 O AHOH 482 24.352 20.291 2.379 0.50 20.49 O HETATM 1536 O BHOH 482 24.181 18.429 1.588 0.50 24.50 O 2. Parallel computing in GROMACS What is the maximum number of computers in parallel computers in Gromacs? There are people on the list better equipped to answer this question. But you might be able to find a number of processors that will be optimal for your case by readin the Gromacs 4 paper and doing some tests. The more computers used in parallel, the less efficiency they have. For example, I want to see the micelle formation in 2 month and the parallel computing will be used. The starting configuration is random-spread of surfactants. The system is = 0.25mM = 300 solutes + so many water molecues (TIP3P water model) What is your suggestion of the number of computers used in parallel computing? I'm sorry, but I can't give an answer to this. If you have constructed your system, you should probably just try different numbers of processors for short (ps) simulations and from that determine what is optimal for your case. Hope it helps :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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: Questions
Chih-Ying Lin wrote: Hi Tsjerk: I still have questions here. 1. Although you have explained the differece between HOH, AHOH and BHOH, I do not fully understand. = Can I delete all of atoms, HOH, AHOH and BHOH ? 2. So, in your tutorial, you use united atom algorithm, right? and, pdb2gmx can recognize the united atoms and give them the proper force fields, right? 3. If one want to use the all-atom algorithm, use the command protonate + protein pdb file first to add all missing hydrogens, then, use pdb2gmx to get an all-atom force field parameters, right? No. just pdb2gmx -ff oplsaa 4. In your last email = where did you get the following information? = I re-check the original 1LW9.pdb = I did not get the information by myself. The answer to this question is in the format specification of the PDB file. The A and B are alternative identifiers and indicate that the electron density can be explained by a water molecule that is partially present at two sites. If you look at the occupancy field you'll notice that the corresponding values are less than 1. In fact, if you sum the occupancies for equivalent atoms in for A and B, they will add up to 1. Thank you very much, Lin On 4/28/09, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lin, I bounce this mail to the gromacs user list as the issues are well off to be archived. I have two stupid questions here. Well, that's up to us to decide ;) 1. I want to get the proper structure of lysozyme. From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL) and 2-hydroxethyl disulfide (HED) are removed. http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ Further, I remove the water, such as HOH, AHOH and BHOH. I don't know what is the differece between HOH, AHOH and BHOH. The answer to this question is in the format specification of the PDB file. The A and B are alternative identifiers and indicate that the electron density can be explained by a water molecule that is partially present at two sites. If you look at the occupancy field you'll notice that the corresponding values are less than 1. In fact, if you sum the occupancies for equivalent atoms in for A and B, they will add up to 1. Then, I add all missing H atoms. = made the new pdb file = it is attached. Would you please take a look if the pdb file is corrct? No, I'm not going to do that. Have a look at the structure to see if it is okay and be sure to take into account whether you used a united atom force field or an all atom one. In your tutorial, why don't you add the missing hydrogen atoms? I do (or rather, I let the students do it ;)). It's one of the things pdb2gmx does. Is it unnecessary to add the missing H atoms? Each residue/molecule should have atoms (with coordinates) matching with the description in the force field used. So if hydrogen atoms are missing with respect to the force field, then they have to be added. HETATM 1504 O HOH 445 36.056 19.096 6.798 1.00 34.30 O HETATM 1535 O AHOH 482 24.352 20.291 2.379 0.50 20.49 O HETATM 1536 O BHOH 482 24.181 18.429 1.588 0.50 24.50 O 2. Parallel computing in GROMACS What is the maximum number of computers in parallel computers in Gromacs? There are people on the list better equipped to answer this question. But you might be able to find a number of processors that will be optimal for your case by readin the Gromacs 4 paper and doing some tests. The more computers used in parallel, the less efficiency they have. For example, I want to see the micelle formation in 2 month and the parallel computing will be used. The starting configuration is random-spread of surfactants. The system is = 0.25mM = 300 solutes + so many water molecues (TIP3P water model) What is your suggestion of the number of computers used in parallel computing? I'm sorry, but I can't give an answer to this. If you have constructed your system, you should probably just try different numbers of processors for short (ps) simulations and from that determine what is optimal for your case. Hope it helps :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 -- 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:
