[gmx-users] infelicity in installation of 4.0.2
Hi all, I've compiled 4.0.2 from source on an EM64T machine running Ubuntu, using ./configure --enable-shared With all executables I've tried, I find: [EMAIL PROTECTED]:~/gromacs/test_installation$ editconf :-) G R O M A C S (-: *** stack smashing detected ***: editconf terminated Segmentation fault [EMAIL PROTECTED]:~/gromacs/test_installation$ which editconf /usr/local/gromacs/bin/editconf [EMAIL PROTECTED]:~/gromacs/test_installation$ /usr/local/gromacs/bin/editconf :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.0.2 (-: i.e. it only runs fine if I specify the full path. Searching the archives, I found that this was reported in April 07, with a reply that it will be fixed in 3.3.2 Nothing more recent came up, but apologies if I missed it. Cheers Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED]* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** ___ 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] REMD problem in concept
Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? I may be missing a very basic point and any suggestion regarding this will be highly helpful. Thanking you, Sarbani ___ 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] cpu parallel
Dear Users I have 2 computer,each mashine has 1 core2quad cpu. I have installed lamm 7,when I run mdrun -np4 on 1 machine cpu usage of 4 cores is over 90% and its s faster than single mode but when I run mdrun on 2 machines ,cpu usage of cores is about 30% and it doesnt get more speed can you help me? my network is gigabit and I connect 2 machines with gigbit cards and crooss cable thank you ___ 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: problems running grompp with protein-ligand complex
Hello. I will try now to send part of my itp file and if another part of the file is needed I will send it if requested. Below are the emails that were already sent regarding my problem. I hope I have not caused any incovenience. Fabrício Bracht I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that: Fatal error: Found a second defaults directive, file ligand.itp, line 5 I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line. I would like some advice on the matter if possible. Thank you in advance Fabrício Bracht Well, it's not like grompp is recognizing you have a ligand there right now, is it? grompp doesn't reach the point where it realizes you don't seem to have a ligand. It seems there's something wrong with the topology. Better post ligand.itp, like Justin suggests, and also give the error which occurs when you do comment out the defaults line in the ligand topology. Cheers, Tsjerk Now, the actual itp file. ; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 c2 c2 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 ce ce 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cf cf 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 [ moleculetype ] ;namenrexcl M_E 3 [ atoms ] ; nr type resi res atom cgnr charge mass typeBchargeB 1o 1M_E O491 -0.55230 16.0 ; qtot -0.552 2c 1M_E C482 0.63200 12.01000 ; qtot 0.080 3 oh 1M_E O503 -0.60900 16.0 ; qtot -0.529 4 ho 1M_E H514 0.44690 1.00800 ; qtot -0.082 5 c3 1M_E C455 -0.12590 12.01000 ; qtot -0.208 6 hc 1M_E H466 0.08080 1.00800 ; qtot -0.127 7 hc 1M_E H477 0.08110 1.00800 ; qtot -0.046 8 c3 1M_E C428 -0.07210 12.01000 ; qtot -0.118 9 hc 1M_E H439 0.06640 1.00800 ; qtot -0.052 10 hc 1M_E H44 10 0.05040 1.00800 ; qtot -0.002 11 c3 1M_E C39 11 -0.05170 12.01000 ; qtot -0.053 12 hc 1M_E H40 12 0.04490 1.00800 ; qtot -0.008 13 hc 1M_E H41 13 0.05410 1.00800 ; qtot 0.046 14 c2 1M_E C37 14 -0.16730 12.01000 ; qtot -0.122 15 ha 1M_E H38 15 0.11950 1.00800 ; qtot -0.002 16 c2 1M_E C35 16 -0.16710 12.01000 ; qtot -0.169 17 ha 1M_E H36 17 0.11730 1.00800 ; qtot -0.052 18 c3 1M_E C32 18 -0.04940 12.01000 ; qtot -0.101 19 hc 1M_E H33 19 0.07250 1.00800 ; qtot -0.029 20 hc 1M_E H34 20 0.06180 1.00800 ; qtot 0.033 21 c3 1M_EC2 21 -0.00340 12.01000 ; qtot 0.030 22 hc 1M_EH6 22 0.07250 1.00800 ; qtot 0.102 23 c2 1M_EC1 23 -0.10390 12.01000 ; qtot -0.002 24 ha 1M_EH8 24 0.14850 1.00800 ; qtot 0.147 25 ce 1M_EC5 25 -0.25360 12.01000 ; qtot -0.107 26 ha 1M_EH9 26 0.16130 1.00800 ; qtot 0.054 27c 1M_EC4 27 0.56070 12.01000 ; qtot 0.615 28o 1M_EO7 28 -0.52650 16.0 ; qtot 0.089 29 ce 1M_EC3 29 -0.21970 12.01000 ; qtot
Re: [gmx-users] infelicity in installation of 4.0.2
Hi, On Tuesday, 2. December 2008, Martyn Winn wrote: Hi all, I've compiled 4.0.2 from source on an EM64T machine running Ubuntu, using ./configure --enable-shared With all executables I've tried, I find: [EMAIL PROTECTED]:~/gromacs/test_installation$ editconf :-) G R O M A C S (-: *** stack smashing detected ***: editconf terminated Segmentation fault [EMAIL PROTECTED]:~/gromacs/test_installation$ which editconf /usr/local/gromacs/bin/editconf [EMAIL PROTECTED]:~/gromacs/test_installation$ /usr/local/gromacs/bin/editconf :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.0.2 (-: i.e. it only runs fine if I specify the full path. Searching the archives, I found that this was reported in April 07, with a reply that it will be fixed in 3.3.2 Nothing more recent came up, but apologies if I missed it. can you paste the output of ldd $your_executable? Have you sourced the GMXRC file? Greetings, Florian -- --- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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: [gmx-users] cpu parallel
ha salem wrote: Dear Users I have 2 computer,each mashine has 1 core2quad cpu. I have installed lamm 7,when I run mdrun -np4 on 1 machine cpu usage of 4 cores is over 90% and its s faster than single mode but when I run mdrun on 2 machines ,cpu usage of cores is about 30% and it doesnt get more speed can you help me? my network is gigabit and I connect 2 machines with gigbit cards and crooss cable As you'll see if you search the GROMACS mailing list archives, gigabit is not normally good enough for acceptable scaling. Your processors are idling while waiting for data to transfer. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] infelicity in installation of 4.0.2
Hi I hadn't source'd the GMXRC file, but that doesn't seem to help. But then I noticed that it ran fine in another terminal window. After a bit of experimentation, it seems to be to do with the length of PATH. In the first terminal, PATH is about 2000 characters long (don't ask ;-) Going to the second terminal where it worked, if I increase the PATH variable by adding /usr/local/gromacs/bin lots of times, I can make that crash too. A bit of grepping in the source code, I notice that gmxlib/futil.c has a few hard limits like char system_path[512] (it seems to strcat onto system_path without checking the length ??). Might this be the problem? For the record: [EMAIL PROTECTED]:~/gromacs/test_installation$ ldd /usr/local/gromacs/bin/editconf linux-vdso.so.1 = (0x7fff2abfc000) libgmxana.so.5 = /usr/local/gromacs/lib/libgmxana.so.5 (0x7f072254a000) libmd.so.5 = /usr/local/gromacs/lib/libmd.so.5 (0x7f0722258000) libgmx.so.5 = /usr/local/gromacs/lib/libgmx.so.5 (0x7f0721db4000) libxml2.so.2 = /usr/lib/libxml2.so.2 (0x7f0721a6d000) libnsl.so.1 = /lib/libnsl.so.1 (0x7f0721854000) libfftw3f.so.3 = /usr/lib/libfftw3f.so.3 (0x7f072159a000) libm.so.6 = /lib/libm.so.6 (0x7f0721319000) libSM.so.6 = /usr/lib/libSM.so.6 (0x7f072000) libICE.so.6 = /usr/lib/libICE.so.6 (0x7f0720ef6000) libX11.so.6 = /usr/lib/libX11.so.6 (0x7f0720bf3000) libc.so.6 = /lib/libc.so.6 (0x7f0720891000) libdl.so.2 = /lib/libdl.so.2 (0x7f072068d000) libz.so.1 = /usr/lib/libz.so.1 (0x7f0720476000) libpthread.so.0 = /lib/libpthread.so.0 (0x7f072025a000) libxcb-xlib.so.0 = /usr/lib/libxcb-xlib.so.0 (0x7f0720059000) libxcb.so.1 = /usr/lib/libxcb.so.1 (0x7f071fe3e000) /lib64/ld-linux-x86-64.so.2 (0x7f07228d9000) libXau.so.6 = /usr/lib/libXau.so.6 (0x7f071fc3c000) libXdmcp.so.6 = /usr/lib/libXdmcp.so.6 (0x7f071fa37000) Cheers Martyn On Tue, 2008-12-02 at 13:52 +0100, Florian Haberl wrote: Hi, On Tuesday, 2. December 2008, Martyn Winn wrote: Hi all, I've compiled 4.0.2 from source on an EM64T machine running Ubuntu, using ./configure --enable-shared With all executables I've tried, I find: [EMAIL PROTECTED]:~/gromacs/test_installation$ editconf :-) G R O M A C S (-: *** stack smashing detected ***: editconf terminated Segmentation fault [EMAIL PROTECTED]:~/gromacs/test_installation$ which editconf /usr/local/gromacs/bin/editconf [EMAIL PROTECTED]:~/gromacs/test_installation$ /usr/local/gromacs/bin/editconf :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.0.2 (-: i.e. it only runs fine if I specify the full path. Searching the archives, I found that this was reported in April 07, with a reply that it will be fixed in 3.3.2 Nothing more recent came up, but apologies if I missed it. can you paste the output of ldd $your_executable? Have you sourced the GMXRC file? Greetings, Florian -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED]* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** ___ 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: [gmx-users] REMD problem in concept
sarbani chattopadhyay wrote: Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. Kinetic energy is a function of the velocities, potential energy is a function of the positions. So velocity rescaling will not have any instantaneous effect on the PE. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? As before, nothing. I may be missing a very basic point and any suggestion regarding this will be highly helpful. Once the simulation continues, things are still normal. The reason the exchange occurred was that the positions were such that the PE was close enough that detailed balance for the generalized ensemble was preserved during the swap. Thus the ensembles before and after the exchange are also still well-formed. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] time of dynamic
would you please tell me for compare dynamic peptide what time for MD is enough by gromacs?generally. You can take your 20 ns simulation, and divide it into 2-4 parts, each 10 (or 5) ns long. Then, calculate the property you are interested in for each part seperately. If 20 ns is more then enought, then the difference between the parts should be minimal. Another option is to calculate the variance of the propery you are calculating, vs. time. --Omer. ___ 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] Cutoff Parameters
Hi, I am sorry that I am repeating an earlier email that I sent out to the list. I did not receive a reply. It would indeed be very useful for me to have some input on this. I am new to gromacs and have a pretty basic question. I am using gromacs-3.3.3 to simulate glycine crystal growth. My system consists of glycine crystal surrounded by a solution of glycine in water (system size: 4.28 by 5.76 by 3.27 nm^3). I have been trying to find appropriate values for the cutoff distances (rvdw, rcoulomb) and corresponding rlist. I use GROMOS96 43a1 force field with PME (pme_order = 4, rtol = 1e-5). The examples given in the gromacs tutorial use rvdw = rlist = rcoulomb = 0.9 (with coulombtype = cutoff). I also found a couple of relevant journal articles that used these parameters. A relevant message on the archive (http://osdir.com/ml/science.biology.gromacs.user/2006-06/msg00389.html) suggests the use of these parameters. Also, Using PME on page 78 of the manual 3.3 suggests rvdw = rlist = rcoulomb = 0.9 However, the manual suggests rvdw = 1.4 for grmos96 force field. When I did a gmx-users list search, I found some mdp files from various users that use vdw = rlist = rcoulomb = 0.9/1.0. Based on sections 7.3.9 and 7.3.10, I think rlist = rcoulomb = 0.9, and rvdw = 1.4 would be appropriate. However, I am not completely sure and it would be great if someone can please recommend a set of values for these parameters (rlist, rvdw, rcoulomb) for coulombtype = PME. Best, Soumik Soumik Banerjee Max-Planck-Institute for Dynamics of Complex Technical Systems Sandtorstraße 1 39106 Magdeburg Germany Email: [EMAIL PROTECTED] Phone: +49 391 6110 163 ___ 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: [gmx-users] Re: problems running grompp with protein-ligand complex
Hi, On Tuesday, 2. December 2008, Ragnarok sdf wrote: Hello. I will try now to send part of my itp file and if another part of the file is needed I will send it if requested. Below are the emails that were already sent regarding my problem. I hope I have not caused any incovenience. Fabrício Bracht You have to combine all atomtypes into one file something like filename ff_atomtypes.itp #define FF_ATOMTYPES [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ; namemass chargeptype sigma epsilon S 0. 0. A 3.56359e-01 1.04600e+00 CC 0. 0. A 3.39967e-01 3.59824e-01 HO 0. 0. A 0.0e+00 0.0e+00 N3 0. 0. A 3.25000e-01 7.11280e-01 all atom types from amber force field 99 and also from your ligand (check if parameters are ok). delete atomtypes and defaults entry in your ligand.itp load in your .top #include ff_atomtypes.itp #include receptor.itp #include ligand.itp ... greetings, Florian I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that: Fatal error: Found a second defaults directive, file ligand.itp, line 5 I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line. I would like some advice on the matter if possible. Thank you in advance Fabrício Bracht Well, it's not like grompp is recognizing you have a ligand there right now, is it? grompp doesn't reach the point where it realizes you don't seem to have a ligand. It seems there's something wrong with the topology. Better post ligand.itp, like Justin suggests, and also give the error which occurs when you do comment out the defaults line in the ligand topology. Cheers, Tsjerk Now, the actual itp file. ; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 c2 c2 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 ce ce 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cf cf 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 [ moleculetype ] ;namenrexcl M_E 3 [ atoms ] ; nr type resi res atom cgnr charge mass typeB chargeB 1o 1M_E O491 -0.55230 16.0 ; qtot -0.552 2c 1M_E C482 0.63200 12.01000 ; qtot 0.080 3 oh 1M_E O503 -0.60900 16.0 ; qtot -0.529 4 ho 1M_E H514 0.44690 1.00800 ; qtot -0.082 5 c3 1M_E C455 -0.12590 12.01000 ; qtot -0.208 6 hc 1M_E H466 0.08080 1.00800 ; qtot -0.127 7 hc 1M_E H477 0.08110 1.00800 ; qtot -0.046 8 c3 1M_E C428 -0.07210 12.01000 ; qtot -0.118 9 hc 1M_E H439 0.06640 1.00800 ; qtot -0.052 10 hc 1M_E H44 10 0.05040 1.00800 ; qtot -0.002 11 c3 1M_E C39 11 -0.05170 12.01000 ; qtot -0.053 12 hc 1M_E H40 12 0.04490 1.00800 ; qtot -0.008 13 hc 1M_E H41 13 0.05410 1.00800 ; qtot 0.046 14 c2 1M_E C37 14 -0.16730 12.01000 ; qtot -0.122 15 ha 1M_E H38 15 0.11950 1.00800 ; qtot -0.002 16 c2 1M_E C35 16 -0.16710 12.01000 ; qtot -0.169 17 ha 1M_E H36 17 0.11730 1.00800 ;
[gmx-users] (no subject)
Dear Users I have 2 computer,each mashine has 1 core2quad cpu. I have installed lamm 7,when I run mdrun -np4 on 1 machine cpu usage of 4 cores is over 90% and its s faster than single mode but when I run mdrun on 2 machines ,cpu usage of cores is about 30% and it doesnt get more speed can you help me? my network is gigabit and I connect 2 machines with gigbit cards and crooss cable thank you ___ 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] Hildebrand's solubility parameter
Hello, could you tell me if it is possible with gromacs to calculate the Hildebrand's solubility parameter? Thank you, Nikos ___ 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: [gmx-users] Hildebrand's solubility parameter
Claus Valka wrote: Hello, could you tell me if it is possible with gromacs to calculate the Hildebrand's solubility parameter? Yes, but you have to derive the components in the equation yourself using g_energy. http://cool-palimpsest.stanford.edu/byauth/burke/solpar/solpar2.html Thank you, Nikos ___ 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 -- 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: +46184714205. Fax: +4618511755. [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 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: [gmx-users] Hildebrand's solubility parameter
Hello,thank you very much for the comprehensive guide. It was quite straighforward, better than others I have come accross. The problem is that I do not still understand which will be the components of the equation from the tools that gromacs provides. From what I have read I have to use the middle value of the difference of :the potential energy of the mother chains and the whole potential energy of the box of the simulation.Could you sed a little bit more light to this?Thank you, Nikos --- David van der Spoel [EMAIL PROTECTED] schrieb am Di, 2.12.2008: Von: David van der Spoel [EMAIL PROTECTED] Betreff: Re: [gmx-users] Hildebrand's solubility parameter An: Discussion list for GROMACS users gmx-users@gromacs.org Datum: Dienstag, 2. Dezember 2008, 16:48 Claus Valka wrote: Hello, could you tell me if it is possible with gromacs to calculate the Hildebrand's solubility parameter? Yes, but you have to derive the components in the equation yourself using g_energy. http://cool-palimpsest.stanford.edu/byauth/burke/solpar/solpar2.html Thank you, Nikos ___ 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 -- 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: +46184714205. Fax: +4618511755. [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 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
Re: Re: [gmx-users] REMD problem in concept
Hi, Thank you for the reply. But in that case what helps the replica at higher temperature cross the energy barrier? At higher temperature the velocities will be higher. Thanks in advance, Sarbani On Tue, 02 Dec 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled after the exchange) comes with a higher energy. It's kinetic energy gets reduced as velocities are rescaled. Thus its potential energy increases. Kinetic energy is a function of the velocities, potential energy is a function of the positions. So velocity rescaling will not have any instantaneous effect on the PE. What happens to the replica that was at lower temperature? It's velocities need to be increased to maintain the temperature. What happens to it's potential energy then? As before, nothing. I may be missing a very basic point and any suggestion regarding this will be highly helpful. Once the simulation continues, things are still normal. The reason the exchange occurred was that the positions were such that the PE was close enough that detailed balance for the generalized ensemble was preserved during the swap. Thus the ensembles before and after the exchange are also still well-formed. 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 [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
[Fwd: Re: [gmx-users] cpu parallel]
Please keep discussions on the mailing list. Mark Original Message Subject: Re: [gmx-users] cpu parallel Date: Wed, 03 Dec 2008 13:08:18 +1100 From: Mark Abraham [EMAIL PROTECTED] To: [EMAIL PROTECTED] References: [EMAIL PROTECTED] ha salem wrote: dear mark I didnt find anything about cpu usage can you help me ?do you think I must change my network cards? they are 1000 mgbps See http://www.google.com.au/search?q=gigabit+site%3Agromacs.org 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
