Re: [gmx-users] acpype generated different tip3p water paramters
Hi Alan, So is acpype using a conversion factor of 4.184 for dihedral force constant? I found some dihedral constants as 0.156 in the amber format, which should be 0.156*4.184=0.652704 in gromacs unit. However, acpype gave a force constant of 0.65084 after conversion, which is slightly off. I wonder if this is OK, and I suspect it might be that I used rdparm to check the amber format value, which only gives 3 decimals for force constants. Thanks for the reply, Yun Hi Yun, ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER. Now why GMX tip3p file choose a different value, I don't know. Nevertheless, it's pretty simple to put whatever value you want there if you think you need. Alan -- 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] acpype generated different tip3p water paramters
Indeed, if you do the other way: 0.65084/4.184 = 0.1 ~ 0.156 Alan On 6 October 2011 08:17, Yun Shi yunsh...@gmail.com wrote: Hi Alan, So is acpype using a conversion factor of 4.184 for dihedral force constant? I found some dihedral constants as 0.156 in the amber format, which should be 0.156*4.184=0.652704 in gromacs unit. However, acpype gave a force constant of 0.65084 after conversion, which is slightly off. I wonder if this is OK, and I suspect it might be that I used rdparm to check the amber format value, which only gives 3 decimals for force constants. Thanks for the reply, Yun Hi Yun, ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER. Now why GMX tip3p file choose a different value, I don't know. Nevertheless, it's pretty simple to put whatever value you want there if you think you need. Alan -- 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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] acpype generated different tip3p water paramters
Hi Yun, ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER. Now why GMX tip3p file choose a different value, I don't know. Nevertheless, it's pretty simple to put whatever value you want there if you think you need. Alan On 26 September 2011 17:35, Yun Shi yunsh...@gmail.com wrote: Hi all, I just noted that the tip3p water converted from amber format to gromacs format is [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834 16.0 2 HW 1 WATH1 1 0.4171.00800 3 HW 1 WATH2 1 0.4171.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 0.09572 462750.4 1 3 1 0.09572 462750.4 0.09572 462750.4 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.520836.800 104.520836.800 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif while in amber99sb.ff/tip3p.itp. it is moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW 1 SOL OW 1 -0.83416.0 2 HW 1 SOL HW1 1 0.417 1.00800 3 HW 1 SOL HW2 1 0.417 1.00800 #ifndef FLEXIBLE [ settles ] ; OWfunct doh dhh 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force_constant 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force_constant 2 1 3 1 104.52 628.02 104.52 628.02 #endif So it seems that the force_constants for O-H bond and H-O-H angle are different? Does this mean amber and gromacs use different parameters for tip3p water? or it's just acpype is not working right? Thanks, Yun -- 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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] acpype generated different tip3p water paramters
Hi all, I just noted that the tip3p water converted from amber format to gromacs format is [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834 16.0 2 HW 1 WATH1 1 0.4171.00800 3 HW 1 WATH2 1 0.4171.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 0.09572 462750.4 1 3 1 0.09572 462750.4 0.09572 462750.4 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.520836.800 104.520836.800 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif while in amber99sb.ff/tip3p.itp. it is moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW 1 SOL OW 1 -0.83416.0 2 HW 1 SOL HW1 1 0.417 1.00800 3 HW 1 SOL HW2 1 0.417 1.00800 #ifndef FLEXIBLE [ settles ] ; OWfunct doh dhh 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force_constant 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force_constant 2 1 3 1 104.52 628.02 104.52 628.02 #endif So it seems that the force_constants for O-H bond and H-O-H angle are different? Does this mean amber and gromacs use different parameters for tip3p water? or it's just acpype is not working right? Thanks, Yun -- 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
