Re: [gmx-users] calculation of density for martini coarse-grained
Hi Sara, For calculation of the density you need the masses. Neither editconf nor genbox uses real masses. They approximate the mass based on a list of atom names and associated masses, which is quite crude and fails if the atoms are not listed. Martini beads are not listed... To get the density you have to look at the .edr file that is written during the simulation. Cheers, Tsjerk On Fri, Dec 16, 2011 at 7:02 AM, mohammad agha mra...@yahoo.com wrote: Excuse me, I did all of examples in my system with different molecules (even water alone) and with different force fields and I took this warning for all of them by doing genbox command!!! WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Is this warning for all in this command, always? If not, then why have I that always? My density is calculated wrong in gromacs and density is important for me! Please help me. Best Regards Sara From: mohammad agha mra...@yahoo.com To: jalem...@vt.edu jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:28 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained Thank you very much. Best Regards Sara From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:02 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Thank you very much for your reply. I experienced genbox for gromos force field for my molecules and for dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same warning for all them!!! May I know that what should I do, Please ? Probably nothing. If you use a coordinate file as input into a number of tools you'll likely get the same. As I said, it is a warning, not an error that needs fixing. It is up to you, as the user, to verify that the output of the program is what you want it to be. Issues related to measured density as you've been reporting are likely a consequence of bizarre atom names that Gromacs doesn't understand. You have to (correctly) do the math to find what the density should be. -Justin Best Regards Sara *From:* Justin A. Lemkul jalem...@vt.edu *To:* mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 9:26 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Dear Prof. Thank you very much. Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. The warning indicates that names may give misleading values for masses and van der Waals interactions. For instance, is CA an alpha-carbon, or calcium? In this context, the program reporting the error doesn't know. Since MARTINI uses lots of weird atom names for its structures, the program is warning you that the output may be incorrect, or perhaps it may not; hence why it is a warning and not an error. -Justin I checked mailing list but I didn't find my answer! Please help me. Best Regards Sara *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 6:31 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume : 1000 (nm^3) Density : 15.8111 (g/l) Number of SOL molecules: 0 One possibility is that the Martini force field doesn't have the masses set up correctly for genbox to match from the coordinate file. Perhaps in share/top/atommass.dat
Re: [gmx-users] calculation of density for martini coarse-grained
Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume : 1000 (nm^3) Density : 15.8111 (g/l) Number of SOL molecules: 0 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 7.4 7.4 7.4 Output of terminal: Read 755 atoms Volume: 1000 nm^3, corresponds to roughly 45 electrons No velocities found system size : 9.803 9.897 9.978 (nm) diameter : 13.969 (nm) center : 5.239 4.900 4.932 (nm) box vectors : 10.000 10.000 10.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1000.00 (nm^3) shift : 2.161 2.500 2.468 (nm) new center : 7.400 7.400 7.400 (nm) new box vectors : 14.800 14.800 14.800 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :3241.79 (nm^3) 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 3- mdrun -v -deffnm e1 4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 output of terminal: Output configuration contains 33306 atoms in 32702 residues Volume : 3241.79 (nm^3) Density : 3070.15 (g/l) Number of SOL molecules: 0 ___ I have a problem about density in step 4 after adding water, again!!! ___ 5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 Analysing residue names: There are: 32702 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 99915.00 This run will generate roughly 49 Mb of data There was 1 note 6- mdrun -v -deffnm e3 7- genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151 output of terminal: Reading file e3.tpr, VERSION 4.5.4 (single precision) Using a coulomb cut-off of 1.2 nm Will try to add 0 NA ions and 151 cl- ions. Select a continuous group of solvent molecules Group 0 ( System) has 33306 elements Group 1 ( Other) has 33306 elements Group 2 ( CA) has 755 elements Group 3 ( W) has 32551 elements Select a group: 3 __ Adding ions was done successfully but in the genion.log file had been written System total charge: 151.000 __ 8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1 output of terminal: WARNING 1 [file topol.top, line 23]: 151 non-matching atom names atom names from topol.top will be used atom names from 4.gro will be ignored Analysing residue names: There are: 32702 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 99915.00 This run will generate roughly 49 Mb of data There was 1 warning My topol.top file is: #include martini_v2.0.itp #include martini_v2.0_ions.itp #include martini_v2.0_lipids.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] CA in water [ molecules ] CA 151 W 32400 cl- 151 ___ Best RegardsSara From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 11:19 AM Subject: Re: [gmx-users] calculation of density for martini coarse-grained On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L
Re: [gmx-users] calculation of density for martini coarse-grained
in water [ molecules ] CA 151 W 32400 cl- 151 ___ Best Regards Sara *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 11:19 AM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, but about density, I think that I am wrong: 151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ), then 755 * 72 amu = 54360 amu, and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!! Please use standard abbreviations for your units unless you want risk people not taking you seriously... I've no idea how you can divide 90254.026*10e-24 by 1000*10e-24 and get 52.23 or 15.8111 And there is the same problem after adding water and ion! May I know my mistake, Please? 2- My surfactant molecule has one positive charge, after I added 151 surfactants, water and antifreezewater, Gromacs answer me that (for each step): NOTE1: system has non-zero total charge: 1.51e+2 Then I added 151 ions to my system with -nn 151 for neutralization, but in the genion.log was reported that System total charge: 151.000!!!, When did genion report that, before or after adding ions? Did the addition succeed? Are your solvent molecules named SOL? but after doing grompp, GROMACS didn't report note about system charge. Is this right? We don't know. Copied and pasted command lines and terminal output are a lot more useful for getting help than sentences describing them. Mark -- 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/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 mailto: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] calculation of density for martini coarse-grained
Dear Prof. Thank you very much. Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. I checked mailing list but I didn't find my answer! Please help me. Best Regards Sara From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 6:31 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume : 1000 (nm^3) Density : 15.8111 (g/l) Number of SOL molecules: 0 One possibility is that the Martini force field doesn't have the masses set up correctly for genbox to match from the coordinate file. Perhaps in share/top/atommass.dat? 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 7.4 7.4 7.4 Output of terminal: Read 755 atoms Volume: 1000 nm^3, corresponds to roughly 45 electrons No velocities found system size : 9.803 9.897 9.978 (nm) diameter : 13.969 (nm) center : 5.239 4.900 4.932 (nm) box vectors : 10.000 10.000 10.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1000.00 (nm^3) shift : 2.161 2.500 2.468 (nm) new center : 7.400 7.400 7.400 (nm) new box vectors : 14.800 14.800 14.800 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :3241.79 (nm^3) So the box volume of 2.gro is not 1000 nm^3. 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 3- mdrun -v -deffnm e1 4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 output of terminal: Output configuration contains 33306 atoms in 32702 residues Volume : 3241.79 (nm^3) Density : 3070.15 (g/l) Number of SOL molecules: 0 ___ I have a problem about density in step 4 after adding water, again!!! Could be the same issue - apparently the water is something like three times as heavy as normal water (whose density is around 1000g/L). ___ 5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 Analysing residue names: There are: 32702 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 99915.00 This run will generate roughly 49 Mb of data There was 1 note 6- mdrun -v -deffnm e3 7- genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151 output of terminal: Reading file e3.tpr, VERSION 4.5.4 (single precision) Using a coulomb cut-off of 1.2 nm Will try to add 0 NA ions and 151 cl- ions. Select a continuous group of solvent molecules Group 0 ( System) has 33306 elements Group 1 ( Other) has 33306 elements Group 2 ( CA) has 755 elements Group 3 ( W) has 32551 elements Select a group: 3 __ Adding ions was done successfully but in the genion.log file had been written System total charge: 151.000 That would be normal before adding ions, and indicative of a problem after adding ions, but you haven't made this clear... You say it was successful, and then announce that it reports a total charge consistent with failure. If genion succeeded in changing some solute to ions, its output is very clear about this. __ 8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1 output of terminal: WARNING 1 [file topol.top, line 23]: 151 non-matching atom names atom names from topol.top will be used atom names
Re: [gmx-users] calculation of density for martini coarse-grained
mohammad agha wrote: Dear Prof. Thank you very much. Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. The warning indicates that names may give misleading values for masses and van der Waals interactions. For instance, is CA an alpha-carbon, or calcium? In this context, the program reporting the error doesn't know. Since MARTINI uses lots of weird atom names for its structures, the program is warning you that the output may be incorrect, or perhaps it may not; hence why it is a warning and not an error. -Justin I checked mailing list but I didn't find my answer! Please help me. Best Regards Sara *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 6:31 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume :1000 (nm^3) Density: 15.8111 (g/l) Number of SOL molecules: 0 One possibility is that the Martini force field doesn't have the masses set up correctly for genbox to match from the coordinate file. Perhaps in share/top/atommass.dat? 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 7.4 7.4 7.4 Output of terminal: Read 755 atoms Volume: 1000 nm^3, corresponds to roughly 45 electrons No velocities found system size : 9.803 9.897 9.978 (nm) diameter: 13.969 (nm) center : 5.239 4.900 4.932 (nm) box vectors : 10.000 10.000 10.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1000.00 (nm^3) shift : 2.161 2.500 2.468 (nm) new center : 7.400 7.400 7.400 (nm) new box vectors : 14.800 14.800 14.800 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :3241.79 (nm^3) So the box volume of 2.gro is not 1000 nm^3. 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 3- mdrun -v -deffnm e1 4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 output of terminal: Output configuration contains 33306 atoms in 32702 residues Volume : 3241.79 (nm^3) Density: 3070.15 (g/l) Number of SOL molecules: 0 ___ I have a problem about density in step 4 after adding water, again!!! Could be the same issue - apparently the water is something like three times as heavy as normal water (whose density is around 1000g/L). ___ 5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 Analysing residue names: There are: 32702 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 99915.00 This run will generate roughly 49 Mb of data There was 1 note 6- mdrun -v -deffnm e3 7- genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151 output of terminal: Reading file e3.tpr, VERSION 4.5.4 (single precision) Using a coulomb cut-off of 1.2 nm Will try to add 0 NA ions and 151 cl- ions. Select a continuous group of solvent molecules Group 0 ( System) has 33306 elements Group 1 ( Other) has 33306 elements Group 2 (CA) has 755 elements Group 3 ( W) has 32551 elements Select a group: 3 __ Adding ions was done successfully but in the genion.log file had been written System total charge: 151.000 That would be normal before adding ions, and indicative of a problem after adding ions, but you haven't made this clear... You say it was successful, and then announce
Re: [gmx-users] calculation of density for martini coarse-grained
mohammad agha wrote: Thank you very much for your reply. I experienced genbox for gromos force field for my molecules and for dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same warning for all them!!! May I know that what should I do, Please ? Probably nothing. If you use a coordinate file as input into a number of tools you'll likely get the same. As I said, it is a warning, not an error that needs fixing. It is up to you, as the user, to verify that the output of the program is what you want it to be. Issues related to measured density as you've been reporting are likely a consequence of bizarre atom names that Gromacs doesn't understand. You have to (correctly) do the math to find what the density should be. -Justin Best Regards Sara *From:* Justin A. Lemkul jalem...@vt.edu *To:* mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 9:26 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Dear Prof. Thank you very much. Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. The warning indicates that names may give misleading values for masses and van der Waals interactions. For instance, is CA an alpha-carbon, or calcium? In this context, the program reporting the error doesn't know. Since MARTINI uses lots of weird atom names for its structures, the program is warning you that the output may be incorrect, or perhaps it may not; hence why it is a warning and not an error. -Justin I checked mailing list but I didn't find my answer! Please help me. Best Regards Sara *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 6:31 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume:1000 (nm^3) Density:15.8111 (g/l) Number of SOL molecules: 0 One possibility is that the Martini force field doesn't have the masses set up correctly for genbox to match from the coordinate file. Perhaps in share/top/atommass.dat? 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 7.4 7.4 7.4 Output of terminal: Read 755 atoms Volume: 1000 nm^3, corresponds to roughly 45 electrons No velocities found system size : 9.803 9.897 9.978 (nm) diameter: 13.969 (nm) center : 5.239 4.900 4.932 (nm) box vectors : 10.000 10.000 10.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1000.00 (nm^3) shift : 2.161 2.500 2.468 (nm) new center : 7.400 7.400 7.400 (nm) new box vectors : 14.800 14.800 14.800 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :3241.79 (nm^3) So the box volume of 2.gro is not 1000 nm^3. 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 3- mdrun -v -deffnm e1 4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 output of terminal: Output configuration contains 33306 atoms in 32702 residues Volume:3241.79 (nm^3) Density:3070.15 (g/l) Number of SOL molecules: 0 ___ I have a problem about density in step 4 after adding water, again!!! Could be the same issue - apparently the water is something like three times as heavy as normal water (whose density is around 1000g/L). ___ 5- grompp -f em.mdp
Re: [gmx-users] calculation of density for martini coarse-grained
Thank you very much. Best Regards Sara From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:02 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Thank you very much for your reply. I experienced genbox for gromos force field for my molecules and for dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same warning for all them!!! May I know that what should I do, Please ? Probably nothing. If you use a coordinate file as input into a number of tools you'll likely get the same. As I said, it is a warning, not an error that needs fixing. It is up to you, as the user, to verify that the output of the program is what you want it to be. Issues related to measured density as you've been reporting are likely a consequence of bizarre atom names that Gromacs doesn't understand. You have to (correctly) do the math to find what the density should be. -Justin Best Regards Sara *From:* Justin A. Lemkul jalem...@vt.edu *To:* mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 9:26 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Dear Prof. Thank you very much. Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. The warning indicates that names may give misleading values for masses and van der Waals interactions. For instance, is CA an alpha-carbon, or calcium? In this context, the program reporting the error doesn't know. Since MARTINI uses lots of weird atom names for its structures, the program is warning you that the output may be incorrect, or perhaps it may not; hence why it is a warning and not an error. -Justin I checked mailing list but I didn't find my answer! Please help me. Best Regards Sara *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 6:31 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume : 1000 (nm^3) Density : 15.8111 (g/l) Number of SOL molecules: 0 One possibility is that the Martini force field doesn't have the masses set up correctly for genbox to match from the coordinate file. Perhaps in share/top/atommass.dat? 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 7.4 7.4 7.4 Output of terminal: Read 755 atoms Volume: 1000 nm^3, corresponds to roughly 45 electrons No velocities found system size : 9.803 9.897 9.978 (nm) diameter : 13.969 (nm) center : 5.239 4.900 4.932 (nm) box vectors : 10.000 10.000 10.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1000.00 (nm^3) shift : 2.161 2.500 2.468 (nm) new center : 7.400 7.400 7.400 (nm) new box vectors : 14.800 14.800 14.800 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :3241.79 (nm^3) So the box volume of 2.gro is not 1000 nm^3. 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr output of terminal: NOTE 1 [file topol.top, line 22]: System has non-zero total charge: 1.51e+02 3- mdrun -v -deffnm e1 4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 output of terminal: Output configuration contains 33306 atoms in 32702 residues Volume : 3241.79 (nm^3) Density : 3070.15 (g/l) Number of SOL molecules: 0
Re: [gmx-users] calculation of density for martini coarse-grained
Excuse me, I did all of examples in my system with different molecules (even water alone) and with different force fields and I took this warning for all of them by doing genbox command!!! WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Is this warning for all in this command, always? If not, then why have I that always? My density is calculated wrong in gromacs and density is important for me! Please help me. Best Regards Sara From: mohammad agha mra...@yahoo.com To: jalem...@vt.edu jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:28 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained Thank you very much. Best Regards Sara From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:02 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Thank you very much for your reply. I experienced genbox for gromos force field for my molecules and for dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same warning for all them!!! May I know that what should I do, Please ? Probably nothing. If you use a coordinate file as input into a number of tools you'll likely get the same. As I said, it is a warning, not an error that needs fixing. It is up to you, as the user, to verify that the output of the program is what you want it to be. Issues related to measured density as you've been reporting are likely a consequence of bizarre atom names that Gromacs doesn't understand. You have to (correctly) do the math to find what the density should be. -Justin Best Regards Sara *From:* Justin A. Lemkul jalem...@vt.edu *To:* mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 9:26 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Dear Prof. Thank you very much. Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. The warning indicates that names may give misleading values for masses and van der Waals interactions. For instance, is CA an alpha-carbon, or calcium? In this context, the program reporting the error doesn't know. Since MARTINI uses lots of weird atom names for its structures, the program is warning you that the output may be incorrect, or perhaps it may not; hence why it is a warning and not an error. -Justin I checked mailing list but I didn't find my answer! Please help me. Best Regards Sara *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 6:31 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why? In the martini_v2.0.itp file, has been written all particle masses are set to 72 amu. May I know my mistake, Please? My solvent molecules aren't named SOL. Command lines and terminal outputs: 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro output of terminal is: Output configuration contains 755 atoms in 151 residues Volume : 1000 (nm^3) Density : 15.8111 (g/l) Number of SOL molecules: 0 One possibility is that the Martini force field doesn't have the masses set up correctly for genbox to match from the coordinate file. Perhaps in share/top/atommass.dat? 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 7.4 7.4 7.4 Output of terminal: Read 755 atoms Volume: 1000 nm^3, corresponds to roughly 45 electrons No velocities found system size : 9.803 9.897 9.978 (nm) diameter : 13.969 (nm) center : 5.239 4.900 4.932 (nm) box vectors : 10.000 10.000 10.000 (nm) box angles : 90.00 90.00 90.00
[gmx-users] calculation of density for martini coarse-grained
Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, but about density, I think that I am wrong: 151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ), then 755 * 72 amu = 54360 amu, and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!! And there is the same problem after adding water and ion! May I know my mistake, Please? 2- My surfactant molecule has one positive charge, after I added 151 surfactants, water and antifreezewater, Gromacs answer me that (for each step): NOTE1: system has non-zero total charge: 1.51e+2 Then I added 151 ions to my system with -nn 151 for neutralization, but in the genion.log was reported that System total charge: 151.000!!!, but after doing grompp, GROMACS didn't report note about system charge. Is this right? Please help me. Best Regards Sara-- 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] calculation of density for martini coarse-grained
On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, but about density, I think that I am wrong: 151 * 5 = 755 beads ( since all particle masses are set to 72 amu in MARTINI ), then 755 * 72 amu = 54360 amu, and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!! Please use standard abbreviations for your units unless you want risk people not taking you seriously... I've no idea how you can divide 90254.026*10e-24 by 1000*10e-24 and get 52.23 or 15.8111 And there is the same problem after adding water and ion! May I know my mistake, Please? 2- My surfactant molecule has one positive charge, after I added 151 surfactants, water and antifreezewater, Gromacs answer me that (for each step): NOTE1: system has non-zero total charge: 1.51e+2 Then I added 151 ions to my system with -nn 151 for neutralization, but in the genion.log was reported that System total charge: 151.000!!!, When did genion report that, before or after adding ions? Did the addition succeed? Are your solvent molecules named SOL? but after doing grompp, GROMACS didn't report note about system charge. Is this right? We don't know. Copied and pasted command lines and terminal output are a lot more useful for getting help than sentences describing them. 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
