Re: [gmx-users] Charge groups
On 5/13/13 8:23 PM, Marcelo Vanean wrote: Hi. I'm with doubts concerning the charge groups. I am simulating ethylene glycol and the only way of charged groups are neutral is putting all atoms in only one charge group. This is advisable? Is that a problem? What is the greatest number of atoms in a charge group which is recommended? Most force fields do not use charge groups (i.e. one atom per charge group) and with PME, there is no requirement that a charge group have an integral charge. -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] charge groups
On 11/5/12 9:24 AM, akn wrote: Dear gmx users, I'm using PME for electrostatic interactions and so I don't need to arrange charge groups. I think the treatment of charge groups relies more on the force field rather than the electrostatics method. With PME, it is true that you do not necessarily need charge groups with integral charge, but not that you can necessarily eliminate charge groups altogether. What force field are you using? I want to learn how should I fill cgnr coloumn if I don't want to arrange charge groups. İf my molecule contains ten atoms, is it enough to write the numbers from 1 to 10 for each atom at the cgnr coulumn? If individual atoms in charge groups are appropriate for your force field, yes. -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] Charge groups for particle insertion
You cannot overcome it, unless you rewrite the code. IIRC, the TPI(C) code only accepts molecules for insertion in the same charge group, as it is stated in the error. Best, João On Fri, Mar 9, 2012 at 11:05 PM, Tina Wang ttw...@princeton.edu wrote: I'm encountering a problem in implementing particle insertion of carbon dioxide in a nanoparticle system. I'm using tabulated potentials, in which I constructed two separate tables (one for nanoparticle-carbon potentials and one for nanoparticle-oxygen potentials). The groomp command required the carbon and oxygen to be in two different charge groups. However, the submission of the test produced an error that read: atoms in the molecule to be inserted cannot belong to multiple charge groups. Put them in the same charge group. I don't know how to overcome this contradiction. Any ideas? Thanks! -- 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] Charge groups in Charmm for lipids
The new GROMACS 4.5.4 version of the CHARMM36 force field files are now uploaded on the GROMACS website contributions section. Just to note that if anyone downloaded the 4.5.4 version uploaded a few hours ago then the atomtypes.atp file was incomplete and should download this new version. Sorry for any problems caused by this. Cheers Tom On 06/08/11 02:28, Thomas Piggot wrote: Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Just as an aside, can you update your C36 with the C27 files for proteins and nucleic acids? That saves us from having to copy the charmm27.ff files for those compounds into charmm36.ff...(since the amino and nucleic acid topologies in charmm36.ff still use nondistinct chargegroups requiring the use of -nochargegrp to pdb2gmx) Thanks -- Dr Thomas Piggot University of Southampton, UK. -- 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] Charge groups in Charmm for lipids
Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Cheers Tom On 06/08/11 00:22, Michael McGovern wrote: Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5. I'm putting it together from pieces of what already exists as suggested in the charmm files. I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology in the 4.5 beta release, but in 4.5.3 and 4.5.4, every atom has its own charge group. So for instace, POPC in the beta release had a topology that began: [ POPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 0 C12 CTL5-0.35 0 C13 CTL5-0.35 0 C14 CTL5-0.35 0 H11 HL 0.250 H12 HL 0.250 H21 HL 0.250 H22 HL 0.250 H23 HL 0.250 H31 HL 0.250 H32 HL 0.250 H33 HL 0.250 H41 HL 0.250 H42 HL 0.250 H43 HL 0.250 C15 CTL2-0.08 1 H51 HAL20.091 H52 HAL20.091 P1 PL 1.502 O3 O2L -0.78 2 O4 O2L -0.78 2 O1 OSL -0.57 2 O2 OSL -0.57 2 C1 CTL2-0.08 3 ... While in 4.5.4 this is [ POPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 1 C12 CTL5-0.35 2 C13 CTL5-0.35 3 C14 CTL5-0.35 4 H11 HL 0.255 H12 HL 0.256 H21 HL 0.257 H22 HL 0.258 H23 HL 0.259 H31 HL 0.2510 H32 HL 0.2511 H33 HL 0.2512 H41 HL 0.2513 H42 HL 0.2514 H43 HL 0.2515 C15 CTL2-0.08 16 H51 HAL20.0917 ... The charge groups do not have integer charge and are all one atom. The beta version has groups that agree with the charmm groups and have integer charge. Was this changed on purpose? The beta version seems correct to me, but am I missing something as to why this change would be made? Thanks -- Dr Thomas Piggot University of Southampton, UK. -- 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] Charge groups in Charmm for lipids
Thanks a lot, I will check that out. From: Thomas Piggot t.pig...@soton.ac.uk To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, August 5, 2011 6:48 PM Subject: Re: [gmx-users] Charge groups in Charmm for lipids Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Cheers Tom On 06/08/11 00:22, Michael McGovern wrote: Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5. I'm putting it together from pieces of what already exists as suggested in the charmm files. I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology in the 4.5 beta release, but in 4.5.3 and 4.5.4, every atom has its own charge group. So for instace, POPC in the beta release had a topology that began: [ POPC ] [ atoms ] N NTL -0.60 0 C11 CTL2 -0.10 0 C12 CTL5 -0.35 0 C13 CTL5 -0.35 0 C14 CTL5 -0.35 0 H11 HL 0.25 0 H12 HL 0.25 0 H21 HL 0.25 0 H22 HL 0.25 0 H23 HL 0.25 0 H31 HL 0.25 0 H32 HL 0.25 0 H33 HL 0.25 0 H41 HL 0.25 0 H42 HL 0.25 0 H43 HL 0.25 0 C15 CTL2 -0.08 1 H51 HAL2 0.09 1 H52 HAL2 0.09 1 P1 PL 1.50 2 O3 O2L -0.78 2 O4 O2L -0.78 2 O1 OSL -0.57 2 O2 OSL -0.57 2 C1 CTL2 -0.08 3 ... While in 4.5.4 this is [ POPC ] [ atoms ] N NTL -0.60 0 C11 CTL2 -0.10 1 C12 CTL5 -0.35 2 C13 CTL5 -0.35 3 C14 CTL5 -0.35 4 H11 HL 0.25 5 H12 HL 0.25 6 H21 HL 0.25 7 H22 HL 0.25 8 H23 HL 0.25 9 H31 HL 0.25 10 H32 HL 0.25 11 H33 HL 0.25 12 H41 HL 0.25 13 H42 HL 0.25 14 H43 HL 0.25 15 C15 CTL2 -0.08 16 H51 HAL2 0.09 17 ... The charge groups do not have integer charge and are all one atom. The beta version has groups that agree with the charmm groups and have integer charge. Was this changed on purpose? The beta version seems correct to me, but am I missing something as to why this change would be made? Thanks -- Dr Thomas Piggot University of Southampton, UK. -- 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/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] Charge groups in Charmm for lipids
On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Just as an aside, can you update your C36 with the C27 files for proteins and nucleic acids? That saves us from having to copy the charmm27.ff files for those compounds into charmm36.ff...(since the amino and nucleic acid topologies in charmm36.ff still use nondistinct chargegroups requiring the use of -nochargegrp to pdb2gmx) Thanks -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South 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] Charge groups in Charmm for lipids
Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS website). There is a DPPG entry in the lipids.rtp file that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Just as an aside, can you update your C36 with the C27 files for proteins and nucleic acids? That saves us from having to copy the charmm27.ff files for those compounds into charmm36.ff...(since the amino and nucleic acid topologies in charmm36.ff still use nondistinct chargegroups requiring the use of -nochargegrp to pdb2gmx) Thanks -- Dr Thomas Piggot University of Southampton, UK. -- 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] charge groups
Gavin Melaugh wrote: Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0. 12.0110 3 CA 1 CGECA 2 -0.1150 12.0110 4 CB 1 CGE :wq CB 2 0. 12.0110 Assuming you fix this, then yes, splitting charge groups can work. Use grompp -pp to see the post-processed topology to make sure everything came out as expected. -Justin 5 CA 1 CGECA 3 -0.1150 12.0110 6 CB 1 CGECB 3 0. 12.0110 7 HC 1 CGEHC 1 0.1150 1.0080 8 CU 1 CGECU 13 0.2650 13.0190 9 NU 1 CGENU 13 -0.5970 14.0070 10 HC 1 CGEHC 2 0.1150 1.0080 11 CU 1 CGECU 14 0.2650 13.0190 12 NU 1 CGENU 14 -0.5970 14.0070 13 HC 1 CGEHC 3 0.1150 1.0080 Cheers Gavin -- 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/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] charge groups
Gavin Melaugh wrote: Hi Justin The two files processed.top and topol.top are the exact same. What is worrying me is that when I look at the topol.tpr from gmxdump, my charge groups do not seem to be specified the way I stated in the topology file. Can you provide a relevant snippet of the gmxdump output to demonstrate this? Consecutive numbering is not stated as a requirement in the manual, and if it is in the code, then it needs to be either documented as being necessary, and/or an enhancement request needs to be filed on redmine for non-consecutive charge group numbering. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0. 12.0110 3 CA 1 CGECA 2 -0.1150 12.0110 4 CB 1 CGE :wq CB 2 0. 12.0110 Assuming you fix this, then yes, splitting charge groups can work. Use grompp -pp to see the post-processed topology to make sure everything came out as expected. -Justin 5 CA 1 CGECA 3 -0.1150 12.0110 6 CB 1 CGECB 3 0. 12.0110 7 HC 1 CGEHC 1 0.1150 1.0080 8 CU 1 CGECU 13 0.2650 13.0190 9 NU 1 CGENU 13 -0.5970 14.0070 10 HC 1 CGEHC 2 0.1150 1.0080 11 CU 1 CGECU 14 0.2650 13.0190 12 NU 1 CGENU 14 -0.5970 14.0070 13 HC 1 CGEHC 3 0.1150 1.0080 Cheers Gavin -- 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/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] charge groups
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3 CA 1 CGECA 2 -0.1150 12.0110
4 CB 1 CGECB 2 0. 12.0110
5 CA 1 CGECA 3 -0.1150 12.0110
6 CB 1 CGECB 3 0. 12.0110
7 HC 1 CGEHC 1 0.1150 1.0080
8 CU 1 CGECU 13 0.2650 13.0190
9 NU 1 CGENU 13 -0.5970 14.0070
10 HC 1 CGEHC 2 0.1150 1.0080
11 CU 1 CGECU 14 0.2650 13.0190
12 NU 1 CGENU 14 -0.5970 14.0070
13 HC 1 CGEHC 3 0.1150 1.0080
14 CU 1 CGECU 15 0.2650 13.0190
15 NU 1 CGENU 15 -0.5970 14.0070
cgs:
nr=112
cgs[0]={0..1}
cgs[1]={2..3}
cgs[2]={4..5}
cgs[3]={6..6}
cgs[4]={7..8}
cgs[5]={9..9}
cgs[6]={10..11}
cgs[7]={12..12}
cgs[8]={13..14}
cgs[9]={15..16}
cgs[10]={17..18}
cgs[11]={19..20}
cgs[12]={21..21}
cgs[13]={22..23}
cgs[14]={24..24}
cgs[15]={25..26}
cgs[16]={27..27}
cgs[17]={28..29}
cgs[18]={30..31}
cgs[19]={32..33}
cgs[20]={34..35}
cgs[21]={36..36}
cgs[22]={37..38}
cgs[23]={39..39}
cgs[24]={40..41}
cgs[25]={42..42}
cgs[26]={43..44}
cgs[27]={45..46}
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
The two files processed.top and topol.top are the exact same. What is
worrying me is that when I look at the topol.tpr from gmxdump, my charge
groups do not seem to be specified the way I stated in the topology
file.
Can you provide a relevant snippet of the gmxdump output to
demonstrate this?
Consecutive numbering is not stated as a requirement in the manual,
and if it is in the code, then it needs to be either documented as
being necessary, and/or an enhancement request needs to be filed on
redmine for non-consecutive charge group numbering.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi all
Do atoms belonging to the same charge group have to be indexed
consecutively in the topology file or can you have the following.
[atoms]
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3 CA 1 CGECA 2 -0.1150 12.0110
4 CB 1 CGE :wq
CB 2 0. 12.0110
Assuming you fix this, then yes, splitting charge groups can work.
Use grompp -pp to see the post-processed topology to make sure
everything came out as expected.
-Justin
5 CA 1 CGECA 3 -0.1150 12.0110
6 CB 1 CGECB 3 0. 12.0110
7 HC 1 CGEHC 1 0.1150 1.0080
8 CU 1 CGECU 13 0.2650 13.0190
9 NU 1 CGENU 13 -0.5970 14.0070
10 HC 1 CGEHC 2 0.1150 1.0080
11 CU 1 CGECU 14 0.2650 13.0190
12 NU 1 CGENU 14 -0.5970 14.0070
13 HC 1 CGEHC 3 0.1150 1.0080
Cheers
Gavin
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Re: [gmx-users] charge groups
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3 CA 1 CGECA 2 -0.1150 12.0110
4 CB 1 CGECB 2 0. 12.0110
5 CA 1 CGECA 3 -0.1150 12.0110
6 CB 1 CGECB 3 0. 12.0110
7 HC 1 CGEHC 1 0.1150 1.0080
8 CU 1 CGECU 13 0.2650 13.0190
9 NU 1 CGENU 13 -0.5970 14.0070
10 HC 1 CGEHC 2 0.1150 1.0080
11 CU 1 CGECU 14 0.2650 13.0190
12 NU 1 CGENU 14 -0.5970 14.0070
13 HC 1 CGEHC 3 0.1150 1.0080
14 CU 1 CGECU 15 0.2650 13.0190
15 NU 1 CGENU 15 -0.5970 14.0070
cgs:
nr=112
cgs[0]={0..1}
cgs[1]={2..3}
cgs[2]={4..5}
cgs[3]={6..6}
cgs[4]={7..8}
cgs[5]={9..9}
cgs[6]={10..11}
cgs[7]={12..12}
cgs[8]={13..14}
cgs[9]={15..16}
cgs[10]={17..18}
cgs[11]={19..20}
cgs[12]={21..21}
cgs[13]={22..23}
cgs[14]={24..24}
cgs[15]={25..26}
cgs[16]={27..27}
cgs[17]={28..29}
cgs[18]={30..31}
cgs[19]={32..33}
cgs[20]={34..35}
cgs[21]={36..36}
cgs[22]={37..38}
cgs[23]={39..39}
cgs[24]={40..41}
cgs[25]={42..42}
cgs[26]={43..44}
cgs[27]={45..46}
Then it seems pretty clear that one cannot have discontinuous charge groups. I
will find somewhere to put this fact in the manual. It may be a useful
enhancement request. If you need these discontinuous charge groups in your
topology, you'll have to reorganize it such that all grouped atoms are consecutive.
-Justin
--
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
--
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Re: [gmx-users] charge groups
O.K cheers
I assume that this is irrelevant in vacuum with no cut-offs
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3 CA 1 CGECA 2 -0.1150 12.0110
4 CB 1 CGECB 2 0. 12.0110
5 CA 1 CGECA 3 -0.1150 12.0110
6 CB 1 CGECB 3 0. 12.0110
7 HC 1 CGEHC 1 0.1150 1.0080
8 CU 1 CGECU 13 0.2650 13.0190
9 NU 1 CGENU 13 -0.5970 14.0070
10 HC 1 CGEHC 2 0.1150 1.0080
11 CU 1 CGECU 14 0.2650 13.0190
12 NU 1 CGENU 14 -0.5970 14.0070
13 HC 1 CGEHC 3 0.1150 1.0080
14 CU 1 CGECU 15 0.2650 13.0190
15 NU 1 CGENU 15 -0.5970 14.0070
cgs:
nr=112
cgs[0]={0..1}
cgs[1]={2..3}
cgs[2]={4..5}
cgs[3]={6..6}
cgs[4]={7..8}
cgs[5]={9..9}
cgs[6]={10..11}
cgs[7]={12..12}
cgs[8]={13..14}
cgs[9]={15..16}
cgs[10]={17..18}
cgs[11]={19..20}
cgs[12]={21..21}
cgs[13]={22..23}
cgs[14]={24..24}
cgs[15]={25..26}
cgs[16]={27..27}
cgs[17]={28..29}
cgs[18]={30..31}
cgs[19]={32..33}
cgs[20]={34..35}
cgs[21]={36..36}
cgs[22]={37..38}
cgs[23]={39..39}
cgs[24]={40..41}
cgs[25]={42..42}
cgs[26]={43..44}
cgs[27]={45..46}
Then it seems pretty clear that one cannot have discontinuous charge
groups. I will find somewhere to put this fact in the manual. It may
be a useful enhancement request. If you need these discontinuous
charge groups in your topology, you'll have to reorganize it such that
all grouped atoms are consecutive.
-Justin
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Re: [gmx-users] charge groups
Gavin Melaugh wrote:
O.K cheers
I assume that this is irrelevant in vacuum with no cut-offs
Or (for reference) with PME, I would suspect, since in this case charge groups
do not have to be net neutral.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3 CA 1 CGECA 2 -0.1150 12.0110
4 CB 1 CGECB 2 0. 12.0110
5 CA 1 CGECA 3 -0.1150 12.0110
6 CB 1 CGECB 3 0. 12.0110
7 HC 1 CGEHC 1 0.1150 1.0080
8 CU 1 CGECU 13 0.2650 13.0190
9 NU 1 CGENU 13 -0.5970 14.0070
10 HC 1 CGEHC 2 0.1150 1.0080
11 CU 1 CGECU 14 0.2650 13.0190
12 NU 1 CGENU 14 -0.5970 14.0070
13 HC 1 CGEHC 3 0.1150 1.0080
14 CU 1 CGECU 15 0.2650 13.0190
15 NU 1 CGENU 15 -0.5970 14.0070
cgs:
nr=112
cgs[0]={0..1}
cgs[1]={2..3}
cgs[2]={4..5}
cgs[3]={6..6}
cgs[4]={7..8}
cgs[5]={9..9}
cgs[6]={10..11}
cgs[7]={12..12}
cgs[8]={13..14}
cgs[9]={15..16}
cgs[10]={17..18}
cgs[11]={19..20}
cgs[12]={21..21}
cgs[13]={22..23}
cgs[14]={24..24}
cgs[15]={25..26}
cgs[16]={27..27}
cgs[17]={28..29}
cgs[18]={30..31}
cgs[19]={32..33}
cgs[20]={34..35}
cgs[21]={36..36}
cgs[22]={37..38}
cgs[23]={39..39}
cgs[24]={40..41}
cgs[25]={42..42}
cgs[26]={43..44}
cgs[27]={45..46}
Then it seems pretty clear that one cannot have discontinuous charge
groups. I will find somewhere to put this fact in the manual. It may
be a useful enhancement request. If you need these discontinuous
charge groups in your topology, you'll have to reorganize it such that
all grouped atoms are consecutive.
-Justin
--
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
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Re: [gmx-users] charge groups
Also. Obviously I arranged the charge groups like this so that they
would be neutral, I just didn't realise that the atoms comprising the
charge groups had to be in sequence.
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0. 12.0110
3 CA 1 CGECA 2 -0.1150 12.0110
4 CB 1 CGECB 2 0. 12.0110
5 CA 1 CGECA 3 -0.1150 12.0110
6 CB 1 CGECB 3 0. 12.0110
7 HC 1 CGEHC 1 0.1150 1.0080
8 CU 1 CGECU 13 0.2650 13.0190
9 NU 1 CGENU 13 -0.5970 14.0070
10 HC 1 CGEHC 2 0.1150 1.0080
11 CU 1 CGECU 14 0.2650 13.0190
12 NU 1 CGENU 14 -0.5970 14.0070
13 HC 1 CGEHC 3 0.1150 1.0080
14 CU 1 CGECU 15 0.2650 13.0190
15 NU 1 CGENU 15 -0.5970 14.0070
cgs:
nr=112
cgs[0]={0..1}
cgs[1]={2..3}
cgs[2]={4..5}
cgs[3]={6..6}
cgs[4]={7..8}
cgs[5]={9..9}
cgs[6]={10..11}
cgs[7]={12..12}
cgs[8]={13..14}
cgs[9]={15..16}
cgs[10]={17..18}
cgs[11]={19..20}
cgs[12]={21..21}
cgs[13]={22..23}
cgs[14]={24..24}
cgs[15]={25..26}
cgs[16]={27..27}
cgs[17]={28..29}
cgs[18]={30..31}
cgs[19]={32..33}
cgs[20]={34..35}
cgs[21]={36..36}
cgs[22]={37..38}
cgs[23]={39..39}
cgs[24]={40..41}
cgs[25]={42..42}
cgs[26]={43..44}
cgs[27]={45..46}
Then it seems pretty clear that one cannot have discontinuous charge
groups. I will find somewhere to put this fact in the manual. It may
be a useful enhancement request. If you need these discontinuous
charge groups in your topology, you'll have to reorganize it such that
all grouped atoms are consecutive.
-Justin
--
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Re: [gmx-users] Charge groups
mohsen ramezanpour wrote: Dear All I read charge groups section in the gromacs manual. I have a question.please let me know it's answer. Is it necessary that our charge groups be made of afew number of atoms? in the other words ,if I have a charge group with 50 atom,Is my results valid? Absolutely not. Short-range Coulombic interactions are based on the centers of charge groups falling within the cutoffs specified in the .mdp file. With a charge group of 50 atoms, you'll be missing countless interactions. I didn't see anywhere in manual to dertermine any extent for number of atoms in charge groups! See examples in the .rtp file and in the primary literature for the force field of interest. It had just noticed we must make charge groups for atoms with total charge of zero,atoms near to eachother in position. Charge groups do not have to have zero charge. They usually have integral charge, but if you're going to be using PME, this is not an absolute requirement. -Justin Thanks in advance Mohsen -- 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/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] Charge groups
mohsen ramezanpour wrote: Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? Look for similar groups in the force field you're using, and refer to the Gromacs manual, section 4.6.2. For example I have a drug of 50 atom(of course along with it's hidrogenes), and all of my data for charges are as 1.3465728 (suppose they are accurate and different to eachother) Sounds like a wildly inappropriate total charge. Is it possible to make charge groups with zero net charge? How?How can I learn these? Is there any server to do this for me? Thanks in advance for your guide. Refer to the documentation of whatever program you're using to do these calculations. Force field parameterization is hard; don't expect immediate success. Even if you can get sensible charges, they still may not be sufficiently accurate within the guidelines of the chosen force field after you've done whatever validation is required. -Justin -- 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/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] Charge groups Coulomb switch - artifacts in radial distribution function. Atom-based or group-based truncation?
Will Glover wrote: Hi, I have constructed a gromacs MD simulation of liquid tetrahydrofuran (at RTP) in which I'm treating each molecule as a charge group. When using a Switch for both the Coulomb and VdW interactions I see artifacts in the radial distribution function of the Oxygen--alpha-carbon (and other pair) distances around the switching region. I understand that these artifacts occur in atom-based truncation schemes and of course PME fixes the problem (see e.g. http://doi.wiley.com/10.1002/jcc.10117); however, I would ultimately like to interface Gromacs with my own mixed quantum/classical code for which the Ewald method is highly nontrivial and a simpler group-based truncation would suffice. Does Gromacs 4.05 only use atom-based truncation, even when charge groups are defined? I was unable to clearly determine this from the manual. If so, is there a work-around to achieve group-based switching that does not involve hacking the code? Gromacs uses charge-group based neighborsearching: if the centers of the charge group are within the cutoff all the interactions are computed. However since you use a shift function the energies beyond 1.3 nm will be zero, the shift function is atom based. Would you have selected a real cut-off then all the atom pairs would be taken into account. What is to be preferred does however depend on the size of your molecule. In this case the molecule is roughly 0.4 nm. My general advice is to make charge groups small, such that you have a homegeneous system. In your case the oxygen with to flanking CH2 groups could be one, and the other two CH2 groups could be in a group each. This way you could also reduce rlist slightly. By the way, if you use nstlist = 1, neighborsearching is done each step, and hence rlist rcoulomb does not make sense. If you set nstlist = 5 or so you do need rlist rcoulomb for proper energy conservation. I have pasted condensed configuration files below for those that are interested... Many thanks in advance! *** mdout.mdp *** ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.004 nsteps = 25 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm_mode= None ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 1 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.625 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = SWITCH rcoulomb_switch = 1.1 rcoulomb = 1.3 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdwtype = Switch ; cut-off lengths rvdw_switch = 1.1 rvdw = 1.3 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Extension of the potential lookup tables beyond the cut-off table-extension = 4 ; Seperate tables between energy group pairs energygrp_table = ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = Nose-Hoover ; Groups to couple separately tc_grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.5 ref_t= 298 ; Pressure coupling Pcoupl = no ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint_algorithm = LINCS ; Do not constrain the start configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs_order = 6 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs_iter = 2 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs_warnangle = 30 ; Convert harmonic bonds to morse potentials morse= no *** thf.itp (note, my THF is rigid and planar, so I use a 3-membered ring and virtual sites to achieve this) *** [ defaults ] ; nbft cr gp fLJ fQQ 1 211 1 [ atomtypes ] ; at mq ptVW O26.51056525660896 -0.500 A 0.3000 0.7112584 T2 22.79841737169552 0.000 A 0. 0.000 CH2A 0.000 0.250 V 0.3800
Re: [gmx-users] charge groups
Liu Shiyong wrote: Fatal error: atoms 4176 and 4182 in charge group 1767 are in different energy groups PDB: ATOM 4176 OG SER A 541 -13.599 44.346 39.228 1.00 0.00 S1 ATOM 4177 N ALA A 542 -12.827 48.211 42.079 1.00 0.00 A1 ATOM 4178 CA ALA A 542 -12.788 48.960 43.342 1.00 0.00 A1 ATOM 4179 C ALA A 542 -12.052 50.279 43.097 1.00 0.00 A1 ATOM 4180 O ALA A 542 -12.096 50.830 41.993 1.00 0.00 A1 ATOM 4181 CB ALA A 542 -12.084 48.160 44.447 1.00 0.00 A1 ATOM 1 N THR B 1 22.984 77.078 8.100 1.00 20.55 TN Using a structure file to understand a topology problem will give you nothing useful. Charge groups are spelled out in the .top, so look there. I suspect you are once again using the wrong structure file for whatever you're doing. This .pdb file does not have any hydrogens, which means that this structure was not processed by pdb2gmx under any force field (even a UA one), and thus will not correspond to your topology whatsoever. -Justin -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu mailto:sy...@ku.edu (shiyong...@ku.edu mailto:shiyong...@ku.edu or liushiy...@ku.edu mailto:liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant 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://www.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] Charge groups, PME and ions
Andreas Kring wrote: Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not possible to make charge groups with a total charge of zero (or and integer number). Is this best solved by using a separate charge group for each atom?... and is this allowed since the charge of such a charge group is not zero? According to the manual, the charge groups are used to make neighbor lists... but these are only important with respect to the computational speed as long as PME is used to deal with electrostatic interactions? Or have I misunderstood this? For such a small molecule you can have separate charge groups for each atom when using PME. Efficiency gains will be minimal when grouping atoms into charge groups. /Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charge groups, PME and ions [SOLVED]
David van der Spoel wrote: Andreas Kring wrote: Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not possible to make charge groups with a total charge of zero (or and integer number). Is this best solved by using a separate charge group for each atom?... and is this allowed since the charge of such a charge group is not zero? According to the manual, the charge groups are used to make neighbor lists... but these are only important with respect to the computational speed as long as PME is used to deal with electrostatic interactions? Or have I misunderstood this? For such a small molecule you can have separate charge groups for each atom when using PME. Efficiency gains will be minimal when grouping atoms into charge groups. Great! Thanks a lot. /Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
