[gmx-users] question about g_tcaf
Dear gromacs users and developers,I have 1 question about the calculation of viscosity using g_tcaf. I got the visc_k.xvg file. According to Berk Hess's report, the k values should be extrapolated to k=0 to obtain the viscosity. The question is (and I'm sorry if this is a silly question), what is "a" in : eta(k) = eta 0 (1-ak^2) ?..can someone help? I couldn't find (or missed) it in the paper.Thank You in advance, MUHAMMAD ALIF MOHAMMAD LATIFLaboratory of Theoretical and Computational ChemistryDepartment of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPM Serdang, SelangorMALAYSIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Thank You for 4.5.4
Dear Gromacs Developers,Just dropping by to say THANK YOU for v4.5.4, surely is updated version of 4.5.3 with all the bugfixes yes?. I'm having problem getting past my university's proxy server to use git. Now hopefully I can continue my research and solve git problems later..Your hard work is greatly appreciated! MUHAMMAD ALIF MOHAMMAD LATIFLaboratory of Theoretical and Computational ChemistryDepartment of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPM Serdang, SelangorMALAYSIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Git tutorial for gromacs
Dear GROMACS users and developersI had a problem calculating 1/viscosity from my energy file. It's been said that the bug have been fixed and the way to get it is through git. I've successfully cloned the gromacs git repo. But I really did not have any experience using git, so I really need the tutorial for gromacs on how to update my gromacs package. The problem is when I try to open gromacs website, this thing came out:-- "Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. If this is a new install, try refreshing - the API is simply taking its time loading up! HTTP Response Status Code: 0 couldn't connect to host" --Tried refreshing a lot of times, still does not work.Any solution? All I really need right now is to update my gromacs package, can anyone guide me step by step on how to update my gromacs package?Thanks in advance, MUHAMMAD ALIF MOHAMMAD LATIFLaboratory of Theoretical and Computational ChemistryDepartment of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPM Serdang, SelangorMALAYSIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] 1/viscosity in g_energy
Dear GROMACS users and developers,I'm having trouble getting values for my 1/viscosity calculation which obtained from g_energy:g_energy -f md1_vis.edr -o md1_vis_1perv.xvgthe output:Statistics over 101 steps [ 0. through 2000. ps ], 1 data setsAll statistics are over 11 pointsEnergy Average Err.Est. RMSD Tot-Drift---1/Viscosity 0 0 0 0 (m s/kg)gcq#310: "Shoot them in the back now" (The Ramones) Have I done something wrong with my simulation? If that's the case, then this is my mdp parameter:cpp = /lib/cppinclude = -I../topintegrator = mddt = 0.002nsteps = 1nstxout = 100nstvout = 100nstlog = 1000nstenergy = 100nstxtcout = 100xtc_grps = System energygrps = System nstlist = 10 ns_type = gridrlist = 1.0; PME chosen as the best option to calculate viscosity ;coulombtype = PMErcoulomb = 1.0rvdw = 1.4pbc = xyztcoupl = berendsentc-grps = System tau_t = 0.1; temperature supposed to set to 20*C @ 293.15 K as reference work ; ref_t = 293.15Pcoupl = nogen_vel = yesgen_temp = 298.15gen_seed = 173529constraints = none; NEMD ;acc_grps = systemaccelerate = 0.1 0.0 0.0cos_acceleration = 0.02Any suggestion are most welcomed and thank you in advance!MUHAMMAD ALIF MOHAMMAD LATIFLaboratory of Theoretical and Computational ChemistryDepartment of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPM Serdang, SelangorMALAYSIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Sorry
Hello, I have a suggestion, why don't you try building your HOME-MADE molecules using PRODRG webserver, it is specially for protein-related molecules, but such structure like those involving hydrocarbon chains can be made by this webserver. This server provide topologies for GROMACS. Good luck with your research! Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_clustsize error
Dear GROMACS users and developers, I have this error when using g_clustsize. Can anyone help me explain this? Reading frame 0 time 14000.001 Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision) Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision) Group 0 (System) has 95851 elements Group 1 (T80) has 1935 elements Group 2 (OLY) has 646 elements Group 3 (SOL) has 93270 elements Group 4 (OLYT80) has 2581 elements Select a group: 4 Selected 4: 'OLYT80' Last frame 1000 time 16000.001 cmid: 1, cmax: 1, max_size: 2581 --- Program g_clustsize, VERSION 3.3.2 Source code file: matio.c, line: 532 Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 --- Comments and suggestions are most welcomed. Thank You Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_clustsize error
Dear GROMACS users and developers, I have this error when using g_clustsize. Can anyone help me explain this? Reading frame 0 time 14000.001 Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision) Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision) Group 0 (System) has 95851 elements Group 1 (T80) has 1935 elements Group 2 (OLY) has 646 elements Group 3 (SOL) has 93270 elements Group 4 (OLYT80) has 2581 elements Select a group: 4 Selected 4: 'OLYT80' Last frame 1000 time 16000.001 cmid: 1, cmax: 1, max_size: 2581 --- Program g_clustsize, VERSION 3.3.2 Source code file: matio.c, line: 532 Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 --- Comments and suggestions are most welcomed. Thank You Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Forming a micelles
Dear Lin, I have suggestions: Micelles should (theoretically) form above the CMC. So if you want a micelle, the concentration should be >>CMC I suggest that you find the CMC experimentally, then convert the concentration to nm^3 (let say: mv/1000nm^3) The number of molecules should be able to obtained by multiplying with Avogadro number: (6.023x10^23). If your system contain co-surfactant, then you'll need to get the experimetal CMC for at least one of the two surfactants (if both non-ionic..if not you'll need the activity coefficient for each surfactant).Take a look at this paper: Bourov G. K. and Bhattacharya A., Brownian dynamics of mixed surfactant micelles, Journal of Chemical Physics, 123 (2005) 204712(1)-204712(6) How long 600 ps simulation is depends on your system size, box type, parameters and computational power (see manual). One other way to KNOW the surfactants formed micelle is by measuring the surface tension (use g_energy). But g_energy gives surface*surface tension value, so you'll need to work on that. (HINT: Surface tension value drop drastically at CMC) Hope these helps, Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Forming a micelles
>Date: Wed, 24 Sep 2008 10:15:44 -0700 >From: "Chih-Ying Lin" <[EMAIL PROTECTED]> >Subject: [gmx-users] Forming a micelles >To: [EMAIL PROTECTED] >Cc: gmx-users@gromacs.org >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1 > >Hi >Would you please say more about your system? >How do you design / decide your simulation size of 100 surfactants +100 >co-surfactants + 4000 water molecules?? > >How many surfactants will form a micelle? >How many atoms does one surfactant have? >How many atoms does one co-surfactant have? > >Do you start from the critical micelle concentration? >You mentioned that it took 3 x 600 ps to see the micelles. >Do you mean that you have 3 computers to do the parallel simulation? > >How long does it take to simulate 600 ps? >Do you visualize the whole 600 ps-image and SEE the micelle? >Or, other technique to KNOW the surfactants forming the micelles >without visualizing the system? > >Thank you >Lin > >** Dear Lin, I have a suggestion: Micelles should (theoretically) form above the CMC. So if you want a micelle, the concentration should be >>CMC I suggest that you find the CMC experimentally, then convert the concentration to nm^3 (let say: mv/1000nm^3) The number of molecules should be able to obtained by multiplying with Avogadro number: (6.023x10^23). If your system contain co-surfactant, then you'll need to get the experimetal CMC for at least one of the two surfactants.Take a look at this paper: Bourov G. K. and Bhattacharya A., Brownian dynamics of mixed surfactant micelles, Journal of Chemical Physics, 123 (2005) 204712(1)-204712(6) How long 600 ps simulation is depends on your system size, box type, parameters and computational power (see manual). One other way to KNOW the surfactants formed micelle is by measuring the surface tension (use g_energy). But g_energy gives surface*surface tension value, so you'll need to work on that. (HINT: Surface tension value drop drastically at CMC) Hope these helps, Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Cluster Size Distribution
Dear GROMACS users and developers, I've succesfully used g_clustsize on my trajectory. But in histo-clust.xvg file, the y-axis parameter is not defined. In the xvg file it only stated as (). Can somebody tell me what legend should be on the y-axis of the graph? Thank You in advance for comments and advices. Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculating average of B-factor
Dear GROMACS users and developers, Sorry for posting same topic again. I really appreciate those replies, thank you. I did use the -res option so i can get the plot rmsf (nm) vs residue. However, with -res option, the bfac.pdb produced include the ANISOU line for each atom (whish is the anistropic temperature factor). The B-factor is still at the end of each atom line. My question is, how can I calculate the average of each residue? here's few line i took form the bfac.pdb:TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 90.072 90.010 90.061 70.58 109.50 70.49 P 1 1 MODEL 1 ATOM 1 N ALA 1 39.870 49.598 31.575 1.00 0.00 ANISOU 1 N ALA 1 27382 16872 28413 -5818 -15784 -6247 ATOM 2 H1 ALA 1 40.270 50.118 30.815 1.00 0.00 ANISOU 2 H1 ALA 1 36121 21080 32250 -8317 -17149 -8021 ATOM 3 H2 ALA 1 40.080 48.628 31.485 1.00 221.02 ANISOU 3 H2 ALA 1 32407 19879 31690 -6481 -17864 -7202ATOM 4 H3 ALA 1 38.870 49.728 31.575 1.00 218.06 ANISOU 4 H3 ALA 1 33154 18573 31125 -6794 -16678 -6289 ATOM 5 CA ALA 1 40.500 50.098 32.805 1.00 168.66 ANISOU 5 CA ALA 1 17671 18590 27822 -3239 -12795 -8333 ATOM 6 CB ALA 1 39.990 49.098 33.845 1.00 220.77 ANISOU 6 CB ALA 1 15699 36171 32009 -10813 -7176 -10100 Can I just average the (B-factor) value at each end of atom line for each residue? Its okay if the B-factor vs redisue plot cant be build. I can use the B-factor vs atoms plot. But people (in papers) have done it (B-fac vs res) before with GROMACS and I'm eager to see the plot for my protein :) "May the Force Fields be with You" - GROMACS Wars Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIAComments, advices and suggestions are greatly appreciated. Thank You. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Plotting B-factor
Dear GROMACS users and developers, I want to plot B-factor of a protein structure against residue. How can I do that?. Using option -oq in g_rmsf only produce bfac.pdb which is in .pdb file and assigned at each atom. Is there another way I can get the plot B-factor vs residue?. Any link to example or tutorial will be very helpful. Comments and Suggestions are greatly appreciated. Thank you. Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem running parallel simulation regarding the md log file
Dear GROMACS users and developers, I've encountered a problem when tying to do a parallel simulation for my protein structure. I tried so many times but the problem still with the log file. Can someone help me out here please?. I changed the log filename, but still got this error: --- Program mdrun_mpi, VERSION 3.3.2 Source code file: futil.c, line: 313 File input/output error: tg1_md.log --- "You Own the Sun" (Throwing Muses) Halting program mdrun_mpi gcq#111: "You Own the Sun" (Throwing Muses) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_2442: p4_error: : -1 p4_error: latest msg from perror: No such file or directory Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Pressure negative after NVT simulation
Dear GROMACS users and developers, I am running MD simulation of lipid self-assembly with total of 53 molecules in a 1000 nm3 cubic simulation box with spc216 as the solvent. After minimization i ran constant NPT MD equilibration up to 1 ns (just to make sure) for the system to have suitable volume and density before running with NVT. After the equilibration, i observed the potential energy and it looked fine. So i took the volume of the equilibration trajectory which then was 1025.51 nm3 as my new box volume. Then i ran 5ns of constant NVT MD simulation. After simulation i checked the pressure of the system throughout the simulation and found that the average pressure of the system from g_energy was -12.7856 bar. The xvg file demonstrated that the pressure fluctuate very high from about 100 to -100 troughout 5 ns. I am still not familiar with this situation but i believe that negative value of pressure is not a good thing. Can anyone kindly help me tell what's wrong with my simulation? Suggestion and comments are greatly appreciated. Thank You. Alif Department of Chemistry, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang, Selangor, MALAYSIA Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about analysing micelle structure
Greetings GROMACS users and developers, I've been studying about the structure of a nanoemulsion of palm-oil and surfactant in water. Many simulations have been performed. My first objective is to replicate the experimental work done and then study the structural properties. I'm using GROMACS (its free, flexible, and fast!!). Simulations produced convincing results; at low composition=no micelle formation, 30% lipid=cylindrical micelle, higher % = two phase (bilayer-like). Its all going the right way until I changed the surfactant with higher HLB value which, (Israelachivli, 2005) theoretically tend to produce spherical micelle. I'm still getting cylindrical, I did simulation with only surfactant and water, (assuming the long-chained oil structure was the culprit). Both surfactants (higher and lower HLV value) still produced cylindrical micelle. My questions are: --Is this got anything to do with my parameters? (in .mdp file?) --Misconcept? Do i need to prepare spherical micelle as the initial structure and then run MD? right now my initial molecules scattered aroung the simulation box randomly. --Can longer simulation time produce spherical? (I've already did 10 ns) I'm pretty confident about the composition of oil and surfactant (experimental data). Could anyone suggest better way? Valid way to do this.. I'm short of experience and no one had done this before right here. Sorry for the long mail. I need help. Thank you very much for reading. Advices, comments and suggestions are greatly welcomed. Thanks again, Alif (Msc. Student) Chemistry Department, Faculty of Science, Universiti Putra Malaysia. Serdang, Selangor, Malaysia. Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Unknown error
Dear GROMACS users, I'm trying to do energy minimization on benzoic acid structure when I got this error: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 1232 of the 1431 non-bonded parameter combinations Cleaning up temporary file gromppX1d9K4 --- Program grompp, VERSION 3.3 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'K' not found! --- I modified the ffgmx2.rtp by including the benzoic acid properties there. Any solution or hint on the problem there? Thanks a lot. Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] re: Self-assembly simulation of lipids
Dear GROMACS users, Thanks for all the replies. They're very helpful. Actually, i have no expertise in this field around me. Moreover i'm from chemistry, so statistical and quantum mechanics are no familiar to me. Thats made my progress become slower (but not impossible right?). I have done several simualtions using the .mdp file that i modify from the example included in the online manual. I'm using the OPLS-AA force field with the reason i'm doing liquid simulations. I have succeeded in doing some simulations (as a practice), got some problems and i solved it most based on these helpful mailing-lists. Its just that i wan to make sure what i'm doing is right until now. I am doing MD simulation on the mixture of Oleyl oleate (palm oil ester) / Sorbitan Monolaurate (Surfactant) in water. The composition is based on experimental results. I packed these molecules using Packmol (excluding water).I added water molecules using genbox in calculated box size. After conjugated-gradients and steepest descents energy minimizations, i run MD simulation. Here's my .mdp file.. any comments and suggestions are very welcomed and helpful. title = MICELLE #7 cpp = cpp include = -I/usr/local/gromacs/share/gromacs/top define = integrator = md dt = 0.001 nsteps = 500 emtol= 50.0 emstep = 0.01 niter = 20 nstcgsteep= 1000 nbfgscorr = 10 nstxout = 5 nstvout = 5 nstlog = 5000 nstenergy = 250 nstxtcout = 250 xtc-precision = 1000 xtc_grps= System energygrps= System nstlist= 10 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = cut-off rcoulomb = 1.2 vdw-type= Cut-off rvdw = 0.8 table-extension = 10.0 pme_order = 4 ewald_rtol = 1e-05 tcoupl = Berendsen tc-grps = System tau_t = 0.1 ref_t = 298 Pcoupl = Berendsen pcoupltype= isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.01325 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints= none Thank You for reading. ----- M. Alif M. Latif Chemistry Department, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia - Got a little couch potato? Check out fun summer activities for kids.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Self-assembly lipid simulation
Dear Gromacs users, I'm doing MD Simulation on self-assembly of lipid molecules using gromacs. If someone can kindly help me find the conditions (for my .mdp file) for these kind of simulation? There are many choices and i would like to ask for opinion on general (usually) conditions used in the .mdp file for the simulation. I would like to look for physical and some thermodynamical properties from my simulation results. This is to aid the experimental results done. Any paper or links also can help me a lot. I have read many papers but i thought maybe u guys can help add more to it. This is because not much options i can find in those papers and not all of them use gromacs.Thanks for reading and your help is greatly appreciated. Thanks again. -- M. Alif M. Latif Chemistry Department, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia - Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem regarding genbox
Dear GROMACS Community, I'm having problem adding spc water molecules into my system containing lipids molecules totaling 64 of them. My simulation box size is 1000 nm^3. I told genbox to fill the simulation box with 100 nm^3 of spc216 water molecules using option (-box 4.642 4.642 4.642) due to the experimental formulation of the mixture. unfortunately, when i view the system, the 100nm^3 of spc216 water that i fill into the box pushed my lipids to each corners of the simulation box. Should i proceed with the simulation or can somebody tell me how to avoid this from happening? Because if the lipids region is at each of the corners, i'm worried about the hydrophobic effect of the lipid structures which i want to study. I wanted the system to be in the box, and the molecules are randomly scattered. last simulation when i used 100 nm^3 simulation box, the lipid structures position and movement exceeded the box in 10 ns of MD simulation. Suggestions and advices are greatly appreciated; Thank You, M. Alif Universiti Putra Malaysia Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: genbox problem with micelle
Dear GROMACS users and developers, Thanks for the response. Just want to add.. my micelle structure, built with Packmol, consists of 10 molecules of Span20 (C18, O6, and 3 polar H) , 90 molecules of oleyl oleate ( C36 , O2 with no polar H). This is the 1:9 ratio of surfactant : oil determined from the experimental results. So my micelle I presume is quite big. I packed the molecules, so that the oils accumulate inside (d = 13) while the surfactant's tail (non-polar) facing to it (d = 14) and the surfactant head (polar groups) facing outside the sphere (d = 19). I've done 1 ns simulation before this, and the water seems to remain in the micelle structure. I'm using a single workstation with Pentium D, 3.0 GHz, and 2Gb of RAM, so I can't manage to get 0.5-1 ns per day. About the vdwradii.dat that you all said, I'll try to do it. But i'm a beginner in this field (I'm a chemist)..It will take time. By the way, I just thought using Packmol to initially arrange the water to be outside the sphere. So I don't have to use genbox. Can I do that? Comments and suggestions are greatly appreciated. Thanks a lot. Alif It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox problem with micelle
Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p Thanks 4 reading...any comments and suggestion will be greatly appreciated.. Alif Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cg error
Dear GROMACS citizens; I'm trying to do a conjugated gradient energy minimization after steepest descent on my structure. But when i executed the grompp, the error came out like this; creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 2 bonded neighbours for SOL 32577 processing coordinates... double-checking input for internal consistency... ERROR: can not do Conjugate Gradients with constraints (97731) --- Program grompp, VERSION 3.3 Source code file: grompp.c, line: 1088 Fatal error: There were 1 error(s) processing your input --- Can somebody tell me what this means?. Is there any limit for number of constraints? Thanks for reading. Advices, clues or suggestions are greatly appreciated..:) Get the free Yahoo! toolbar and rest assured with the added security of spyware protection. http://new.toolbar.yahoo.com/toolbar/features/norton/index.php___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to avoid pdb2gmx from deleting duplicates?
Hi there, Thanks for the last reply, sorry i made a mistakes when writing previous mail. I ran several tests, that's why the output is micelle_3.top and not micelle_1 like i state in the command. If my pdb2gmx command was right (regardless what file name for .gro and .top i put ) , and the structure i get from the PRODRG (for surfactant and oil) is good (i've checked), why the pdb2gmx program deleted the duplicates for surfactant and not for oil? Is there any specifications for the pdb2gmx program to delete duplicates? These duplicates generated using packmol software. Is that the problem? by the way, the .top file referred to the .itp file correctly. Suggestions, ideas, and advices are greatly appreciated. Thanks a lot :) Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Surfactant molecules missing after genbox
Hi everyone, Firstly thanks to Stephane for replying my mail. I've checked the memory and solve the problem. unfortunately, there's another problem.. After i minimize the micelle structure using steepest descent , I ran MD. But when I observed the trajectory, there's only one surfactant molecule left on the structure ( supposed to be 100 !!) There supposed to be 20 oil structure, 100 surfactant plus spc water from genbox. When i look back, the surfactants started missing after i converted the .pdb file to .top and .gro file using pdb2gmx. I built the structure using Packmol. The output .pdb file from the packmol program looks fine. I wonder how this happened. I use this command for pdb2gmx; "pdb2gmx -f micelle_1.pdb -o micelle_1.gro -p micelle_1.top" There were no warning at all, making me more confused. I found that the program deleted the duplicated surfactants. Why the program didn't delete the oil's duplicates?. The surfactants pdb file i got from PRODRG webserver. Can some body give me any idea? Thanks a lot.. --- Back Off! I just backed up micelle_3.top to ./#micelle_3.top.2# Processing chain 1 'A' (380 atoms, 10 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Checking for duplicate atoms Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully No N- or C-terminus found: this chain appears to contain no protein Now there are 10 residues with 380 atoms Chain time... Back Off! I just backed up micelle_3_A.itp to ./#micelle_3_A.itp.1# Making bonds... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Number of bonds was 370, now 370 Generating angles, dihedrals and pairs... Before cleaning: 360 pairs Before cleaning: 360 dihedrals Keeping all generated dihedrals There are 360 dihedrals,0 impropers, 370 angles 360 pairs, 370 bonds and 0 virtual sites Total mass 4643.948 a.m.u. Total charge 0.000 e Writing topology Back Off! I just backed up posre_A.itp to ./#posre_A.itp.1# Processing chain 2 'B' (2700 atoms, 1 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Checking for duplicate atoms Now there are 27 atoms. Deleted 2673 duplicates. Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully No N- or C-terminus found: this chain appears to contain no protein Now there are 1 residues with 27 atoms Chain time... Back Off! I just backed up micelle_3_B.itp to ./#micelle_3_B.itp.1# Making bonds... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Number of bonds was 27, now 27 Generating angles, dihedrals and pairs... Before cleaning: 34 pairs Before cleaning: 39 dihedrals Keeping all generated dihedrals There are 39 dihedrals,0 impropers, 32 angles 34 pairs, 27 bonds and 0 virtual sites Total mass 315.218 a.m.u. Total charge -0.000 e Writing topology Back Off! I just backed up posre_B.itp to ./#posre_B.itp.1# Including chain 1 in system: 380 atoms 10 residues Including chain 2 in system: 27 atoms 1 residues Now there are 407 atoms and 11 residues Total mass in system 4959.166 a.m.u. Total charge in system 0.000 e Writing coordinate file... Back Off! I just backed up micelle_3.pdb to ./#micelle_3.pdb.1# - PLEASE NOTE You have succesfully generated a topology from: mixed_sphere.pdb. The oplsaa force field and the spc water model are used. Note that the default mechanism for selecting a force fields has changed, starting from GROMACS version 3.2.0 - ETON ESAELP Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. http://farechase.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to check memoryuse limit?
Dear GROMACS users, I'm having problem using genbox while trying to solvate my micelle structure. The program produced error "cannot allocate memory". I checked the mailing list archive, and found that Dr. David once told to check the limit command. I tried to type "limit" but the command was not found. Do I need to move to specific directory to use this command? I'm using OS Kernel: Linux version 2.6.9-34.ELsmp (Red Hat 3.4.5-2). Or Maybe something wrong anywhere else?.. I've include the error message (just in case). Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7 Reading solute configuration Built with Packmol Containing 787 atoms in 21 residues Initialising van der waals distances... Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 54x54x54 boxes --- Program genbox, VERSION 3.3 Source code file: smalloc.c, line: 137 Fatal error: realloc for atoms_solvt->atom (-213500416 bytes, file gmx_genbox.c, line 399, at oms_solvt->atom=0x0x 81f07a0) --- "We Don't Bother Anyone" (LIVE) : Cannot allocate memory You snooze, you lose. Get messages ASAP with AutoCheck in the all-new Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_html.html___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Self-Assembly Method
Hi GROMACS users, I'm trying to simulate number of esters together with surfactants which experimentally known will self-assembly into micellar aggregates. I don't know if my method is right, but i put these molecules into one pdb file using VegaZZ software. Then if I successfully edited the topologies and managed to run MD simulation on it, are my results valid? Or do I have to specify other parameters/files/options specially for this kind of interactions? Because its a self-assembly process (driven by the hydrophobic effect), I believed there's no need for me to specify which atoms on the corresponding molecules to interact, right? Thanks a lot, Alif. __ 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 search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD simulation of 2 molecules in a system
Dear GROMACS users, I was wondering if GROMACS can run MD simulation of two molecules in one system (box+spc water). This two molecules have the hydrophobic and polarity effects which i want to see through the simulation. Can anybody suggest how to do it? I cant find it in the manual (or maybe i missed them). Any suggestion will be welcomed and very much appreciated. Thanks a lot.. Alif. 8:00? 8:25? 8:40? Find a flick in no time with the Yahoo! Search movie showtime shortcut. http://tools.search.yahoo.com/shortcuts/#news___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
