[gmx-users] diffusion coefficient of oxygen molecule
Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] diffusion coefficient of oxygen molecule
Sunil Thapa skrev: Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal Hi, I do know that there are finite size effects that affects the diffusion coefficient, so you should make sure you use a big enough box. Furthermore, for water polarizability has an impact on the diffusion coefficient, so if you want to reproduce experimental values, consider using a polarizable model. -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] diffusion coefficient of oxygen molecule
Hi, If i remember correctly SPC/E water might be worth trying. There is plenty of research paper in this field. Try this paper http://pubs.acs.org/doi/abs/10.1021/jp003020w Also P,T coupling have effects on Diffusion Coeff. amit On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa mephy...@yahoo.com wrote: Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] Turn-off water optimisation
Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Turn-off water optimisation
Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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: diffusion coefficient of oxygen molecule
Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal Many guys enjoy SPCE. Its diffusion constant is lower than those of the models you mentioned, if I'm not mistaken. -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Turn-off water optimisation
Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Turn-off water optimisation
Hi, I have never heard about problems like this before. It seems highly unlikely to me that the innerloops are causing this. Are your running exacly the same tpr file on your local machine and the cluster? You probably want to update to version 4.0.7 to be sure you have all the latest bugfixes. Please keep us updated on this issue, since things like this should never happen (unless there is a compiler bug). Berk Date: Fri, 5 Mar 2010 14:41:02 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] Turn-off water optimisation Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Turn-off water optimisation
Hi, Can you also post your .mdp? Ran Berk Hess wrote: Hi, I have never heard about problems like this before. It seems highly unlikely to me that the innerloops are causing this. Are your running exacly the same tpr file on your local machine and the cluster? You probably want to update to version 4.0.7 to be sure you have all the latest bugfixes. Please keep us updated on this issue, since things like this should never happen (unless there is a compiler bug). Berk Date: Fri, 5 Mar 2010 14:41:02 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] Turn-off water optimisation Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] pdb gro files
Hi, please I'm having a problem while running a minimisation. I prepared my system with pdb2gmx and generated .pdb files. From the last pdb file, I did grompp generated the tpr file that I used to start my minimization. At the 46th step, I encountered the problem:water molecule cannot be settled. I looked at the pdb file and found that many water residues have the same number because above residue , it restarts to count residue 0, 1, etc... I prepared the same system but I generated .gro files instead of .pdb started my minimization. But did't encounter the same problem. I looked at the gro file here, it's the atomic number that can't be above 9. So did anyone encounter this problem before, if yes, please do you have a solution to propose? Thanks Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] pdb gro files
I don't think the atom number is the problem. I also have systems with more than 9 atoms, and in the gro file the atom number after 9 is reset to 0, but that was never a problem for the simulations. I would check the parameters again, but I don't have a more exact answer to your problem. 2010/3/5 Carla Jamous carlajam...@gmail.com Hi, please I'm having a problem while running a minimisation. I prepared my system with pdb2gmx and generated .pdb files. From the last pdb file, I did grompp generated the tpr file that I used to start my minimization. At the 46th step, I encountered the problem:water molecule cannot be settled. I looked at the pdb file and found that many water residues have the same number because above residue , it restarts to count residue 0, 1, etc... I prepared the same system but I generated .gro files instead of .pdb started my minimization. But did't encounter the same problem. I looked at the gro file here, it's the atomic number that can't be above 9. So did anyone encounter this problem before, if yes, please do you have a solution to propose? Thanks Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] Turn-off water optimisation
with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100305/011ae49c/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 71, Issue 32 * -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Turn-off water optimisation
Hi all, to summerize the seems really like a compiler problem. i have now compiled 4.0.5 with gcc and had no problems. i don't really know which icc compiler it was (but had send the guy who installed gromacs a mail), but with 'which icc' i find: /share/apps/intel/cce/9.1.046/bin/icc i will try now 4.0.7 with the icc compiler Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] NVT simulation and mdp file
Hi Justin, That is really confusing. I tried to run this PDB file many times. But still I could not get it the topology file. I waited for so long (10 hrs)but still the code looks in a deadlock. Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading JUsti.pdb... Read 'Tolene.pdb', 7 atoms Opening library file /usr/local/gromacs/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 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp Atomtype 1 [1]+ Stopped REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb ATOM1 CB PHE 1 -1.158 0.001 0.000 C ATOM2 CG PHE 1 -1.158 -1.336 0.000 C ATOM3 CD1 PHE 1 -0.000 -2.004 0.000 C ATOM4 CD2 PHE 1 1.158 -1.336 0.000 C ATOM5 CE1 PHE 1 1.158 0.001 0.000 C ATOM6 CE2 PHE 1 -0.000 0.670 0.000 C ATOM7 CZ PHE 1 -0.000 2.167 0.000 C END can you please tell me what modifications you have done so that your pdb2gmx works fine. thank you for your time Rob Quoting Justin A. Lemkul jalem...@vt.edu: tekle...@ualberta.ca wrote: Hi Justin, Thank you pointing out that! I made all the changes and still cannot go past this line. REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb HETATM1 CB PHE 0 -1.158 0.001 0.000 C HETATM2 CG PHE 0 -1.158 -1.336 0.000 C HETATM3 CD1 PHE 0 -0.000 -2.004 0.000 C HETATM4 CD2 PHE 0 1.158 -1.336 0.000 C HETATM5 CE1 PHE 0 1.158 0.001 0.000 C HETATM6 CE2 PHE 0 -0.000 0.670 0.000 C HETATM7 CZ PHE 0 -0.000 2.167 0.000 C END As you can see I used this PDB file but still no topology out put. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be
Re: [gmx-users] NVT simulation and mdp file
tekle...@ualberta.ca wrote: Hi Justin, That is really confusing. I tried to run this PDB file many times. But still I could not get it the topology file. I waited for so long (10 hrs)but still the code looks in a deadlock. Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading JUsti.pdb... Read 'Tolene.pdb', 7 atoms Opening library file /usr/local/gromacs/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 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp Atomtype 1 [1]+ Stopped REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb ATOM1 CB PHE 1 -1.158 0.001 0.000 C ATOM2 CG PHE 1 -1.158 -1.336 0.000 C ATOM3 CD1 PHE 1 -0.000 -2.004 0.000 C ATOM4 CD2 PHE 1 1.158 -1.336 0.000 C ATOM5 CE1 PHE 1 1.158 0.001 0.000 C ATOM6 CE2 PHE 1 -0.000 0.670 0.000 C ATOM7 CZ PHE 1 -0.000 2.167 0.000 C END can you please tell me what modifications you have done so that your pdb2gmx works fine. I assumed the blank lines between each ATOM entry were a consequence of my email client; is your .pdb file actually double-spaced? If so, that's the wrong format. Other than that, I have no idea, it worked fine for me. Does pdb2gmx correctly work on other .pdb files? -Justin thank you for your time Rob Quoting Justin A. Lemkul jalem...@vt.edu: tekle...@ualberta.ca wrote: Hi Justin, Thank you pointing out that! I made all the changes and still cannot go past this line. REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb HETATM1 CB PHE 0 -1.158 0.001 0.000 C HETATM2 CG PHE 0 -1.158 -1.336 0.000 C HETATM3 CD1 PHE 0 -0.000 -2.004 0.000 C HETATM4 CD2 PHE 0 1.158 -1.336 0.000 C HETATM5 CE1 PHE 0 1.158 0.001 0.000 C HETATM6 CE2 PHE 0 -0.000 0.670 0.000 C HETATM7 CZ PHE 0 -0.000 2.167 0.000 C END As you can see I used this PDB file but still no topology out put. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
[gmx-users] Gromacs 4.0.6 installation error
I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --enable-sse --prefix=[mypath] make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Dian -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Gromacs 4.0.6 installation error
Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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] Gromacs 4.0.6 installation error
Actually, I tried 4.0.7 first from this link, http://www.gromacs.org/index.php?title=Download_%26_Installation It didn't work (same error). That's why I downloaded 4.0.6 from the same webpage. On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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://lists.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] Gromacs 4.0.6 installation error
Dian Jiao wrote: Actually, I tried 4.0.7 first from this link, http://www.gromacs.org/index.php?title=Download_%26_Installation It didn't work (same error). That's why I downloaded 4.0.6 from the same webpage. Well, downgrading is usually not the answer, especially if you're downgrading to a broken distribution. Maybe this should be removed from the downloads page... In any case, if a Makefile wasn't generated, then the configuration can't be OK. Some error must have come up. Check the screen output and config.log, if necessary. Once you have an actual error message, you stand to get better advice on how to fix it. -Justin On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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] isopropanol parameters?
Dear GROMACS users, I am simulating aqueous isopropanol. Unfortunately I observe segregation of isopropanol from SPC water at isopropanol fraction volume of 0.25. Since isopropanol is miscible in water, my parameters stress too much the hydrophobic character of this solute. Only a few interstitial waters are present in the isopropanol cluster, in order to saturate the hydrogen bonds of the isopropanol hydroxyl groups. If anybody has good isopropanol parameters for simulation in aqueous environment, please let me know. Best regards, Jose M. Borreguero -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] isopropanol parameters?
On 2010-03-05 20.51, Jose Borreguero wrote: Dear GROMACS users, I am simulating aqueous isopropanol. Unfortunately I observe segregation of isopropanol from SPC water at isopropanol fraction volume of 0.25. Since isopropanol is miscible in water, my parameters stress too much the hydrophobic character of this solute. Only a few interstitial waters are present in the isopropanol cluster, in order to saturate the hydrogen bonds of the isopropanol hydroxyl groups. If anybody has good isopropanol parameters for simulation in aqueous environment, please let me know. Best regards, Jose M. Borreguero Which ones did you use? OPLS will be miscible I'm sure, since I did 1-propanol sims at 11 concentrations from 0 to 100 Mass%. (With TIP4P). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] problem with icc compiler
Hi, i observed the following problem. if i simulate water (spc or tip4p) with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the wrong temperature (ref_t = 300K - average around 425K, in about 1-2ps), but only in serial, not in parallel runs. non-water molecules or nose-hoover thermostat make no problems. see also http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html for mdp and log file. gromacs was compiled with the following comands: and in the file 'configure' all '-lmkl' were deleted (don't ask me why, i don't really understand that stuff, the command were from our previous phd student). ./configure CC=icc CPPFLAGS=-I/share/apps/intel/mkl/10.0.011/include LDFLAGS=-L/share/apps/intel/mkl/10.0.011/lib/em64t -lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread --with-fft=mkl --prefix=/share/apps/gromacs/4.0.5 make make install make clean ./configure CC=icc CPPFLAGS=-I/share/apps/intel/mkl/10.0.011/include LDFLAGS=-L/share/apps/intel/mkl/10.0.011/lib/em64t -lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread --with-fft=mkl --prefix=/share/apps/gromacs/4.0.5 --enable-mpi --disable-nice --program-suffix=_mpi make mdrun make install-mdrun for gromacs 4.0.5 i used the icc 9.1.046 compiler. i also tried gromacs 4.0.7 with icc 9.1.046 and icc 10.1.008 with spc water, v-rescale thermostat. - serial: too high temperature 425K iso 300K - parallel: no problems with non-water (mesitylene) i have no problem in serial. the problem does not come from grompp because i can use same tpr-file for serial and parallel runs with the above results. if someone needs more informations about this please tell me. greetings thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] isopropanol parameters?
I am using SPC/E water model. Regarding isopropanol, these are the partial charges: H10.038594 C10.147250 HC1 0.038591 C2-0.106023 HC2 0.038591 HC3 0.038591 HA1 0.038591 C3-0.106023 HA2 0.038591 HA3 0.038591 O1-0.579340 HO1 0.373996 And the VdW radii and epsilon: HC 1.3770 0.0150 OH 1.7210 0.2104 CT 1.9080 0.1094 HO 0.0 0.0 On Fri, Mar 5, 2010 at 3:21 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2010-03-05 20.51, Jose Borreguero wrote: Dear GROMACS users, I am simulating aqueous isopropanol. Unfortunately I observe segregation of isopropanol from SPC water at isopropanol fraction volume of 0.25. Since isopropanol is miscible in water, my parameters stress too much the hydrophobic character of this solute. Only a few interstitial waters are present in the isopropanol cluster, in order to saturate the hydrogen bonds of the isopropanol hydroxyl groups. If anybody has good isopropanol parameters for simulation in aqueous environment, please let me know. Best regards, Jose M. Borreguero Which ones did you use? OPLS will be miscible I'm sure, since I did 1-propanol sims at 11 concentrations from 0 to 100 Mass%. (With TIP4P). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.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] Gromacs 4.0.6 installation error
On 6/03/2010 5:05 AM, Dian Jiao wrote: Actually, I tried 4.0.7 first from this link, http://www.gromacs.org/index.php?title=Download_%26_Installation It didn't work (same error). That's why I downloaded 4.0.6 from the same webpage. On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| Don't enable threads. Do follow an actual installation guide like on the GROMACS webpage. Mark make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto: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://lists.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] pdb gro files
On 6/03/2010 1:19 AM, Carla Jamous wrote: Hi, please I'm having a problem while running a minimisation. I prepared my system with pdb2gmx and generated .pdb files. From the last pdb file, I did grompp generated the tpr file that I used to start my minimization. At the 46th step, I encountered the problem:water molecule cannot be settled. I looked at the pdb file and found that many water residues have the same number because above residue , it restarts to count residue 0, 1, etc... I prepared the same system but I generated .gro files instead of .pdb started my minimization. But did't encounter the same problem. I looked at the gro file here, it's the atomic number that can't be above 9. So did anyone encounter this problem before, if yes, please do you have a solution to propose? Just use .gro files for these intermediate output files. There are very limited reasons to want .pdb for such intermediate output, such as visualization. If your visualization program can't read .gro, either get a new one (e.g. VMD), or use editconf to convert .gro - .pdb before visualization. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Gromacs 4.0.6 installation error
I got it to work finally. Didn't install fftw earlier. Thanks. On Fri, Mar 5, 2010 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 6/03/2010 5:05 AM, Dian Jiao wrote: Actually, I tried 4.0.7 first from this link, http://www.gromacs.org/index.php?title=Download_%26_Installation It didn't work (same error). That's why I downloaded 4.0.6 from the same webpage. On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| Don't enable threads. Do follow an actual installation guide like on the GROMACS webpage. Mark make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto: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://lists.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://lists.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
