[gmx-users] RE: Gromacs 4.0 beta1
What is the link to download binaries and source code for Gromacs 4.0 beta1? Type in google gromacs CVS -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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: DMSO-protein simulation
how to calculate c6 c12 coloumn for DMSO thanx in advance Search for C6 and C12 for DMSO or for sigma and epsilon in the literature. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] PME 3dc geometry and the optimal PME mesh load
Hi all, I use 3dc geometry for a system with large box size in z direction, and when I try the new CVS version, I find a note saying The optimal PME mesh load is usually between 025 and 0.33, you should probably increase the cut-off and the PME grid spacing. A quite large estimation 0.86 was reported in grompp, and I wonder if I can do sth to speed up the simulation. Thanks for your suggestions in advance. ___ 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: gmx-users Digest, Vol 53, Issue 90
Hi Ran Thank you for your reply. I'm sorry that I miss the message. (1) 6 eigenvalues represent rotation and translation. For (very) small molecules, these can be quite substantial, see Carlsson and Aqvist, /J. Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the rotation and translation. You can search the literature for papers that discuss the QH approximation as well. The motions are not really harmonic - this is why it's an approximation. I've received very similar results to Carlsson and Aqvist for benzene and palmatic acid with GMX. (2) The values you get depend on the sampling and the conversion of the simulations. To improve sampling, you have to store the coordinates frequently enough (so you get more samples). In addition, the simulation should be long enough to give you meaningful results - and both depend on the system which you study. Checking for convergence can be done by repeating the calculations on different time windows, as you suggested. Sorry, I don't quite catch your mind. How to get the convergence variation of the entropy? Whether or not the time split method is right? eg, time points: 0, 1, 2, 3, 4, 5. and time stage：0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? The method of covariance matrix QH can estimate the up-limit of entropy, how to know the error band ? Thank you very much. (3) In entropy calculations, a system need to run a long time for entropy convergence, the time seems to be longer than the one which needed for energy convergence. While, for equilibrium thermodynamics simulations, how to justify whether or not the system has achieving a equilibrium stage, based on energy convergence or entropy confvergence? (4) For the example mentioned in the paper Ioan Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy calculation. But I don't reproduce the result. The needed time of entropy convergence is longer than the time mentioned in the paper, and so larger of my entropy. I don't know why, perphas the simulation conditions is not right. My simulation files are included in the attachment. Could you give some suggestions? BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does 10^-18 mean nm^-2? ___ 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
Re: Re: [gmx-users] Re: Leaflet of Bilayer
Thanks for the response Just diverting this topic to about specific number of popc molecules. I created the bilayer by using genconf command genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I posted in my previous mail) generated output file contain 128 popc in each leaflet of bilayer. If you see original popc box dimensions 6.1x6.2x6.9 (means in all dimensions popc number almost same)but with genconf command above mentioned options created box values 12x6.1x6.9. I dont want that many popc molecules because in X-dimension too many popc molecules are present. 1.is there anyway to reduce those popc molecules from 128 to 80/90 popc molecules? or 2.I wanted to create popc molecules 80 or 90 in eachleaflet is it possible to generate? These are may be trivial queries Could you give suggest me please Thanks in advance. Thanks Justin and Nicolas for gave suggestions. I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this [atomselect top name P8 and z0] num it has showed 201, means the total number popc molecues in the .gro file. Could you tell any suggestion It's probably because your system is not center on 0.0. By default, Gromacs center boxes on lenght/2 It's probably because your system is not centered on 0.0. By default, Gromacs centers boxes on lenght/2 .. Sorry for the grammar, I'm not well awake this morning. Thanks in advance. e Hi Jochen thanks for your reply I have gone through this recent mail http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html more over if I use genconf command like this genconf -f .gro -o out -nbox 2 1 1 -dist 0 0 0 its adding 128 in eachleaflet I dont wany that many popc molecules. 1.Is it wrong if I increase the popc molecules by using genbox? It is best to use genconf, because then the periodic images of the unit cell remain intact, that is, since you're using a pre-equilibrated bilayer, it's better to not snip chunks out of it. You can deal with that by sufficient equilibration, however. It is also easier to use genconf, because you then know exactly how many lipids you are dealing with (in regards to your previous message). You could probably write some script to tell you which lipid is in a given leaflet based on whether a certain atom (i.e., P8 or something else) is above or below the center of the bilayer. In case you use VMD, you can get the number of phospholipid per leaflet with the following command: [atomselect top name P8 and z0] num This will give you the number of PC in the upper leaflet, assuming 1) the phosphorus atom is named P8 and 2) the bilayer is center on 0.0 along the z axis. Nicolas 2.Is there anyway to increase popc and water numbers by mentioning specific molecules number? Not that I'm aware of. There is a -maxsol option in genbox, but that is for capping the amount of water molecules added to a box. -Justin Could you suggest me Thanks in advance. On Fri, 19 Sep 2008 Jochen Hub wrote : minnale wrote: Hi all, I have extended popc bilayer(intial popc.pdb from Dr.Tielmen site) by using genbox command, I issued genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran successfully with increase of popc and water molecules. Now I want to visualise this out file in VMD in a way that in eachleaflet how many popc molecules and water residues are there, May be this is trivial query. Could you give me suggestion. If you want to enlarge a membrane patch, use genconf. Not genbox! jochen Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ 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 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 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!
[gmx-users] How to implement v-rescale thermostat in gromacs-3.3.3
Hi gmx-users, When I came across the 4.0 beta version, I found there was a new thermostat named v-rescale available here. I wonder if it would be easy to incorporate it in the version 3.3.3 as a patch. Note that the 4.0 version is still under development, I prefer to use a revised 3.3.3 version to make a production run. Thanks very much for your help. ___ 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] Cann't get the same result ?
Hi all: I run mdrun of gromacs-3.3.3 6 times of a small simulation, but I cann't get the same result every time. I run the mdrun program using ./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc md1.job ./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc md1.job ./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc md1.job. Three simulations one time. And run two times. The 6 log files are in the accessory. Can someone tell me why cann't I get the same result of the 6 simulations? Appreciate any help in advance! Best wishes! Ji Xu [EMAIL PROTECTED] 2008-09-22 ___ 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 many water molecule used to run MD?
Hi how many water molecules used to run MD? what is the criteria for this? I found some water.gro including 216 or 512 water molecules. Is it enough to include 216 or 512 water molecules only in MD system? For TIP4P; there are 4 coordinates to determine a water molecule. For TIP5P; there are 5 coordinates to determine a water molecule. If I want to include more than 1000 TIP4P or TIP5P water molecules in my MD system, how could I construct the TIP4P.gro and TIP5P.gro files ? Thank you Lin ___ 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] TIP4P and TIP5P
Hi Could anyone tell me how to construct the solvent box of TIP4P and TIP5P model? And, how to construct water_TIP4P.itp and and water_TIP5P.itp ? Thank you very much Lin ___ 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] Multiple ppa files from a single parallel mdrun_mpi job
After taking a closer look at the code, I suspect that the problem can be resolved as follows. The call to: read_pullparams(pull, opt2fn(-pi,nfile,fnm), opt2fn(-po,nfile,fnm)); in pullinit.c should probably be protected by: if (MASTER(cr)) I have not tested this as it doesn't really matter to the run, but it should probably be fixed for 4.0 as it gives the impression that something is wrong (at least it did worry me personally). This may have already been fixed in 3.3.2/3.3.3/cvs, I did not check. Chris. --- original message --- Hello, I am running gromacs in parallel on a new system. I am also using the pull code. Everything appears to be going fine, except that I get backup copies of the .ppa files during a single call to mdrun_mpi. My best guess is that this is some type of mpi problem, but any pointers would be welcomed. Thanks, Chris. Here is the relevant output from mdrun_mpi Reading file adw1.0.tpr, VERSION 3.3.1 (single precision) Reading parameter file this.ppa Reading parameter file this.ppa Reading parameter file this.ppa Reading parameter file this.ppa Groups: r_1 Reference Group: r_2 Using 1 pull groups Using distance components 1 1 0 Back Off! I just backed up adw1.0.ppa to ./#adw1.0.ppa.1# Sorry couldn't backup adw1.0.ppa to ./#adw1.0.ppa.1# Sorry couldn't backup adw1.0.ppa to ./#adw1.0.ppa.1# Groups: r_1 Reference Group: r_2 Using 1 pull groups Using distance components 1 1 0 Groups: r_1 Reference Group: r_2 Using 1 pull groups Using distance components 1 1 0 Groups: r_1 Reference Group: r_2 Using 1 pull groups Using distance components 1 1 0 starting mdrun 'test' 1000 steps, 2.0 ps. ___ 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] Leaflet of Bilayer
In my opinion, use any technique that you want (genbox included) then run the resulting system for =50ns while plotting the area per lipid and order parameters over time. When these values stop drifting over time then you have an equilibrated bilayer. If you have access to a cluster that scales well to 4 cores then this should not take longer than a month. With systems that scale well to 10 cores I can equilibrate such a system in under two weeks. Of course, the more limited your resources are then the more thought that you need to put into your setup. Very generally, for beginners with at least moderate computational resources, I suggest immediately following your first good idea to get the system prepared and then, while it is running, starting to think about how it could have been done in a better way. With cpu resources as they are now, your initial run is likely to be finished faster than anything else if you start it immediately and the next time you go about this it will be faster because you will figure out the better method. Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I as a reader am not going to have any problem with your final results even if I think that you could have obtained an equilibrated bilayer with a quicker method. Important note: Please use a new subject for a new topic. I know that topics often diverge, but you started this thread with a vmd-list question and now you are on to something that is only related to that by the fact that you study membranes. Chris. --- original message --- Thanks for the response Just diverting this topic to about specific number of popc molecules. I created the bilayer by using genconf command genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I posted in my previous mail) generated output file contain 128 popc in each leaflet of bilayer. If you see original popc box dimensions 6.1x6.2x6.9 (means in all dimensions popc number almost same)but with genconf command above mentioned options created box values 12x6.1x6.9. I dont want that many popc molecules because in X-dimension too many popc molecules are present. 1.is there anyway to reduce those popc molecules from 128 to 80/90 popc molecules? or 2.I wanted to create popc molecules 80 or 90 in eachleaflet is it possible to generate? These are may be trivial queries Could you give suggest me please Thanks in advance. ___ 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
