Re: [gmx-users] Expanding existing biphastic Box
On 18/06/2012 3:46 PM, James Starlight wrote: Dear Gromacs Users! I have biphastic system wich consist of Ccl4 layer between 2 layers of water with the dimensions 8 6 10. I want to expand this box on Y dimension from 6 to 8 nm in both ccl4 and water layers. Is there any trivial ways to do add new Ccl4 and solvent molecules to the existing system with the preservation of the density in each layer in accordance to the initial system? genconf -h 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
Dear Sir/Madam Thanks for all the help. I have removed the older version of gromacs and the new one also and hve reinstalled gromacs again. But I am still encountering the same problem. I am unable to figure out. First I removed the installed gromacs and all the links. The set of commands that I have given to install gromacs are as folllows: * ./configure --enable-mpi --program-suffix=_mpi make make mdrun -j 8 make install make install-mdrun make links export PATH=$PATH:/usr/local/gromacs/bin/GMXRC echo $PATH* Please note that initially I had problems while compiling gromacs so I reinstalled fftw (version 3.3.2) by giving in the following commands: *cd fftw-3.3.2 ./configure --enable-float --enable-sse --enable-shared make make install* Please help. I am unable to figure out what's wrong with the installation. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
Nidhi, To get reply from the gmx community, you need to post the error messages which erupts while compiling. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Jun 18, 2012 at 11:43 AM, Nidhi Jatana nidhijat...@bic-svc.ac.inwrote: Dear Sir/Madam Thanks for all the help. I have removed the older version of gromacs and the new one also and hve reinstalled gromacs again. But I am still encountering the same problem. I am unable to figure out. First I removed the installed gromacs and all the links. The set of commands that I have given to install gromacs are as folllows: * ./configure --enable-mpi --program-suffix=_mpi make make mdrun -j 8 make install make install-mdrun make links export PATH=$PATH:/usr/local/gromacs/bin/GMXRC echo $PATH* Please note that initially I had problems while compiling gromacs so I reinstalled fftw (version 3.3.2) by giving in the following commands: *cd fftw-3.3.2 ./configure --enable-float --enable-sse --enable-shared make make install* Please help. I am unable to figure out what's wrong with the installation. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
Dear Sir/Madam I am not getting any errors while compiling. Its all running fine. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Code precision is double message
So getting an error message when tying to run an MD simulation created in 4.0.5 on 4.5.5 These are the steps I followed, and help would be appreciated untared FFTW-3.3.1 ./configure --enable-threads --enable-float --prefix=$home/fftw-3.3.1 make make install untared gromacs-4.5.5 export CPPFLAGS=-I$home/fftw-3.3.1/include/ export LDFLAGS=-L$home/fftw-3.3.1/lib ./configure --prefix=$home/gromacs-4.5.5 --disable-shared make make install No issues up to this point, no error message or anything. When I try to run the following $home/gromacs-4.5.5/bin/mdrun -s md_11.tpr -cpi md_10.cpt -cpo md_11.cpt I get the following error message --- Program mdrun, VERSION 4.5.5 Source code file: checkpoint.c, line: 546 Fatal error: Precision mismatch for state entry nosehoover-xi, code precision is double, file precision is float For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- View this message in context: http://gromacs.5086.n6.nabble.com/Code-precision-is-double-message-tp4998649.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
Ok. You need to source the GMXRC file Follow http://www.gromacs.org/Documentation/Installation_Instructions For bash shell: if your executables are in /usr/local/gromacs/bin $source /usr/local/gromacs/bin/GMXRC Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Jun 18, 2012 at 11:54 AM, Nidhi Jatana nidhijat...@bic-svc.ac.in wrote: Dear Sir/Madam I am not getting any errors while compiling. Its all running fine. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun -v output
Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -v output
Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2 verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s md.tpr verbose.txt Javier El 18/06/12 08:49, Chandan Choudhury escribió: Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
i am doing protein in bilipid membrane simulation. while packing the protein in the lipid membrane step, i am getting this error. command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 300. please help!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem regarding installation of gromacs-4.5.5
On 6/18/12 2:13 AM, Nidhi Jatana wrote: Dear Sir/Madam Thanks for all the help. I have removed the older version of gromacs and the new one also and hve reinstalled gromacs again. But I am still encountering the same problem. I am unable to figure out. First I removed the installed gromacs and all the links. The set of commands that I have given to install gromacs are as folllows: * ./configure --enable-mpi --program-suffix=_mpi make make mdrun -j 8 make install make install-mdrun make links export PATH=$PATH:/usr/local/gromacs/bin/GMXRC echo $PATH* Your installation procedure is wrong. Please follow the instructions here: http://www.gromacs.org/Documentation/Installation_Instructions -Justin Please note that initially I had problems while compiling gromacs so I reinstalled fftw (version 3.3.2) by giving in the following commands: *cd fftw-3.3.2 ./configure --enable-float --enable-sse --enable-shared make make install* Please help. I am unable to figure out what's wrong with the installation. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021. -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] (no subject)
On 6/18/12 4:55 AM, ankita oindrila wrote: i am doing protein in bilipid membrane simulation. while packing the protein in the lipid membrane step, i am getting this error. command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 300. This error usually comes up when there is something wrong with the format of the input .gro file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] hello
Hi This is Anik. Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The DNA consisted of a total 10 base pairs. But within the simulation the DNA is moving inside the solvation box and sometimes it is going outside of the box, though due to NVT simulation criteria the part going out from one side comes back from the other side. But the problem is in a certain step it looks awkward that part of DNA lying here and part lying there. I have taken bigger boxes but with the same result. Can anyone suggest how to overcome this problem? The interaction of the DNA with the water molecules may not hamper but it may not dance so much in the solvation box. Thanx in advance Anik Sen. Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hello
On 18/06/2012 7:46 PM, Anik Sen wrote: Hi This is Anik. Please choose an email subject more descriptive of your problem. That's your chance to attract attention! Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The DNA consisted of a total 10 base pairs. But within the simulation the DNA is moving inside the solvation box and sometimes it is going outside of the box, though due to NVT simulation criteria the part going out from one side comes back from the other side. But the problem is in a certain step it looks awkward that part of DNA lying here and part lying there. I have taken bigger boxes but with the same result. Can anyone suggest how to overcome this problem? The interaction of the DNA with the water molecules may not hamper but it may not dance so much in the solvation box. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hello
On 6/18/12 5:46 AM, Anik Sen wrote: Hi This is Anik. Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The DNA consisted of a total 10 base pairs. But within the simulation the DNA is moving inside the solvation box and sometimes it is going outside of the box, though due to NVT simulation criteria the part going out from one side comes back from the other side. But the problem is in a certain step it looks awkward that part of DNA lying here and part lying there. I have taken bigger boxes but with the same result. Can anyone suggest how to overcome this problem? The interaction of the DNA with the water molecules may not hamper but it may not dance so much in the solvation box. This topic seems to come up every day. Consult the following page and/or the many recent threads in the list archive: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Code precision is double message
On 18/06/2012 4:30 PM, Allen Mao wrote: So getting an error message when tying to run an MD simulation created in 4.0.5 on 4.5.5 These are the steps I followed, and help would be appreciated untared FFTW-3.3.1 ./configure --enable-threads --enable-float --prefix=$home/fftw-3.3.1 make make install untared gromacs-4.5.5 export CPPFLAGS=-I$home/fftw-3.3.1/include/ export LDFLAGS=-L$home/fftw-3.3.1/lib ./configure --prefix=$home/gromacs-4.5.5 --disable-shared make make install No issues up to this point, no error message or anything. When I try to run the following $home/gromacs-4.5.5/bin/mdrun -s md_11.tpr -cpi md_10.cpt -cpo md_11.cpt I get the following error message --- Program mdrun, VERSION 4.5.5 Source code file: checkpoint.c, line: 546 Fatal error: Precision mismatch for state entry nosehoover-xi, code precision is double, file precision is float For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Apparently the checkpoint file format in version 4.0.5 cannot be read properly by 4.5.5. Since the algorithms are slightly different in each GROMACS version, you don't want to do this anyway. Start a new simulation. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -v output
On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo j...@um.es wrote: Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2 verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s md.tpr verbose.txt Thanks. It is actually mdrun -v -s md.tpr verbose.txt Javier El 18/06/12 08:49, Chandan Choudhury escribió: Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Checking interaction energies - regd
Dear Gromacs users, I am using buckingham potential in my simulations for that I have copied charmm27.ff to my working directory, and have modified it, to know whether it is working properly or not, I have run one step simulations and checked the energies obtained in simulations with the energies obtained in the programs that I have written to calculate these energies, In this case non-bonded and dihedral energies are matching perfectly, and am getting a difference of bond stretching energy 1.74 Kj/mol per bond and a large variation in bending energies i.e 56.4 kj/mol per angle, for bending i have used function type 1 and included same functional form i.e 0.5*Ktheta*(theta-theta0)^2 in my program and I have used all the units according to Gromacs conventions in my programs. Can anyone please explain the reason for difference. Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Solvation Free Energy calculation (g_bar)
Hi everyone, I'm having problems when calculating Free energy through the g_bar tool. I'm trying to decouple separately the electrostatic and the Vdw terms. So, after performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1 steps: 0.0-0.1-0.2...0.9-1.0) and the same for the LJ-terms, I'm applying the g_bar for all md*.xvg output files, from both decoupling steps, all together. I mean I join the md*.xvg files from the two decouplings and apply g_bar only once. As a result I'm getting a warning message informing that some results violate the Secong law of Thermodynamics and the error estimation is about 8 KJ/mol! On the other hand, when I apply the g_bar tool separately for the two decouplings I no longer violate the Second Law and the errors are more feasible (~0.3 KJ/mol), however I don't know how the join the two results in order to get the solvation Free energy of the whole process (considering that this is possible, I don't know this as well). Any idea? Daniel. -- View this message in context: http://gromacs.5086.n6.nabble.com/Solvation-Free-Energy-calculation-g-bar-tp4998662.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Solvation Free Energy calculation (g_bar)
On 6/18/12 10:41 AM, Daniel wrote: Hi everyone, I'm having problems when calculating Free energy through the g_bar tool. I'm trying to decouple separately the electrostatic and the Vdw terms. So, after performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1 steps: 0.0-0.1-0.2...0.9-1.0) and the same for the LJ-terms, I'm applying the g_bar for all md*.xvg output files, from both decoupling steps, all together. I mean I join the md*.xvg files from the two decouplings and apply g_bar only once. As a result I'm getting a warning message informing that some results violate the Secong law of Thermodynamics and the error estimation is about 8 KJ/mol! On the other hand, when I apply the g_bar tool separately for the two decouplings I no longer violate the Second Law and the errors are more feasible (~0.3 KJ/mol), however I don't know how the join the two results in order to get the solvation Free energy of the whole process (considering that this is possible, I don't know this as well). Since free energy is a state function, you simply take the sums of the two processes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Solvation Free Energy calculation (g_bar)
Hi Justin, Thank you for your reply. I see what you mean, but the problem is when I use the approach you mentioned (adding the DGs) my result is far from the experimental one, whereas when I choose the first one (which violate the Second law) my result is quite good, except for the error estimation and the warning, It seems that it makes an important difference the way the g_bar is applied, considering my simulations are right. Now I'm trying to increase the number of lambdas in the region where the Second law has been violated in an attempt to solve this issue, Anyway, I'm stil not sure if my procedure is correct and why I'm getting such a difference when applying the g_bar in these two ways. Daniel -- View this message in context: http://gromacs.5086.n6.nabble.com/Solvation-Free-Energy-calculation-g-bar-tp4998662p4998664.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Solvation Free Energy calculation (g_bar)
On 6/18/12 3:05 PM, Daniel wrote: Hi Justin, Thank you for your reply. I see what you mean, but the problem is when I use the approach you mentioned (adding the DGs) my result is far from the experimental one, whereas when I choose the first one (which violate the Second law) my result is quite good, except for the error estimation and the warning, It seems that it makes an important difference the way the g_bar is applied, considering my simulations are right. Now I'm trying to increase the number of lambdas in the region where the Second law has been violated in an attempt to solve this issue, Anyway, I'm stil not sure if my procedure is correct and why I'm getting such a difference when applying the g_bar in these two ways. The warnings you are receiving arise because you're concatenating dissimilar data sets (one where LJ are being decoupled, and one where Coulombic interactions are being decoupled) and expecting the result to make sense. It is possible to (de)couple both LJ and Coulombic terms simultaneously, but I have never done this myself; I have always relied on a two-state (de)coupling procedure. As to the quality of the result, I can't comment on that because I don't know what you're working with. The quality of the result is dependent upon the quality of the topology, so if you're trying to develop new parameters for a molecule, you may need to reconsider how the parameters were derived. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -v output
It actually depends on your shell/environment :-P On sun grid engine and derivatives, the you can have the scheduler capture the stdout and stderr output through the -o and -e parameters, respectively. On 2012-06-18 05:28:11PM +0530, Chandan Choudhury wrote: On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo j...@um.es wrote: Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2 verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s md.tpr verbose.txt Thanks. It is actually mdrun -v -s md.tpr verbose.txt Javier El 18/06/12 08:49, Chandan Choudhury escribió: Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -v output
Thanks Peter for the clarification. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 19, 2012 at 2:27 AM, Peter C. Lai p...@uab.edu wrote: It actually depends on your shell/environment :-P On sun grid engine and derivatives, the you can have the scheduler capture the stdout and stderr output through the -o and -e parameters, respectively. On 2012-06-18 05:28:11PM +0530, Chandan Choudhury wrote: On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo j...@um.es wrote: Information messages, such as those shown on the screen during mdrun are output to stderr. So if you want to get them you should redirect as follows: mdrun -v -s md.tpr 2 verbose.txt In the case where you may need to get all output (from both stdout and stderr) you should use: mdrun -v -s md.tpr verbose.txt Thanks. It is actually mdrun -v -s md.tpr verbose.txt Javier El 18/06/12 08:49, Chandan Choudhury escribió: Dear gmx users, Is it possible to redirect the output of mdrun -v to a file while submitting the job using pbs script? mdrun -v -s md.tpr verbose.txt donot produce output (to file verbose.txt) while the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
