Re: [gmx-users] too much warnings and notes
Hi, On Oct 29, 2012, at 3:57 PM, Albert wrote: > On 10/29/2012 03:56 PM, Carsten Kutzner wrote: >> Hi, >> >> find the reason for the warnings in your mdp file settings >> and adjust them accordingly. >> >> You can also override the warnings with the -maxwarn >> option in grompp. >> >> Carsten > Hello Carsten: > > thanks for kind reply. > > the only thing I confused is the last one: > > NOTE 4 [file md.mdp]: > The sum of the two largest charge group radii (0.597592) is larger than > rlist (1.00) - rvdw (1.20) this is explained here: http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb Carsten > > > > -- > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] too much warnings and notes
On 10/29/12 10:57 AM, Albert wrote: On 10/29/2012 03:56 PM, Carsten Kutzner wrote: Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn option in grompp. Carsten Hello Carsten: thanks for kind reply. the only thing I confused is the last one: NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) It is related to Note 3, which indicates you have a very large charge group. You will have artifacts related to neighbor searching (and potentially poor energy conservation) if you use such large groups. There is discussion on this note on the Gromacs website and in the list archive. I post the link to the Errors page daily, so surely you can find it :) -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] too much warnings and notes
On 10/29/2012 03:56 PM, Carsten Kutzner wrote: Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn option in grompp. Carsten Hello Carsten: thanks for kind reply. the only thing I confused is the last one: NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) -- 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] too much warnings and notes
Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn option in grompp. Carsten On Oct 29, 2012, at 3:52 PM, Albert wrote: > hello: > > I am generating a .tpr file for proten/ligand system, but it has so much > warnings: > > > NOTE 1 [file md.mdp]: > nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting > nstcomm to nstcalcenergy > > > NOTE 2 [file md.mdp]: > leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 > > Generated 23436 of the 23436 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 20254 of the 23436 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'LIG' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'POPC' > turning all bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'NA' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'CL' > turning all bonds into constraints... > Setting gen_seed to 6947582 > Velocities were taken from a Maxwell distribution at 300 K > > NOTE 3 [file complex.top]: > The largest charge group contains 12 atoms. > Since atoms only see each other when the centers of geometry of the charge > groups they belong to are within the cut-off distance, too large charge > groups can lead to serious cut-off artifacts. > For efficiency and accuracy, charge group should consist of a few atoms. > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. > > Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34 > Number of degrees of freedom in T-Coupling group POPC is 33353.66 > Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00 > Largest charge group radii for Van der Waals: 0.299, 0.299 nm > Largest charge group radii for Coulomb: 0.299, 0.299 nm > > NOTE 4 [file md.mdp]: > The sum of the two largest charge group radii (0.597592) is larger than > rlist (1.00) - rvdw (1.20) > > -- > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] too much warnings and notes
hello: I am generating a .tpr file for proten/ligand system, but it has so much warnings: NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 23436 of the 23436 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 20254 of the 23436 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'LIG' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 6947582 Velocities were taken from a Maxwell distribution at 300 K NOTE 3 [file complex.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34 Number of degrees of freedom in T-Coupling group POPC is 33353.66 Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00 Largest charge group radii for Van der Waals: 0.299, 0.299 nm Largest charge group radii for Coulomb: 0.299, 0.299 nm NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) -- 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
