[gmx-users] Is there anyone who has tip3p.gro?
Hi there, Recently, I cannot add tip3p water in my system, because GMX cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has tip3p.gro, and could you please give me one copy. highly appreciate!! shijun -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] Re: gmx-users Digest, Vol 65, Issue 122
Thanks for Mark's fast reply, and It really works. Then, I have another qusetion about the manual: It seems that the exclusion just excludes the nonbond potential of LJ interaction, but Buckingham. If we want to turn off all VDW interaction between some atoms, the energy monitor group is a nice choice. I have no idea if I got it right. And, we can't use LJ and Buckingham in a same system. Unfortunately, I met a force-field that most of the nonbond interactions were described by Buckingham, but LJ only for Ow-Ow among water. I chose nbfunct=2 in [defaults] section,and nbfunct=1 in [nonbond_params] for Ow-Ow. As a result, a error message read: *Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR). *I don't know whether it could be settled in gromacs. Sincerely Shijun -- Message: 1 Date: Mon, 21 Sep 2009 06:24:34 + (GMT) From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: who can help me with the force-field? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: fbcb8a00405b.4ab71...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 09/21/09, xiao shijun xshi...@gmail.com wrote: Mark wrote: xiao shijun wrote: Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! Usually you would not define a nonbonded interaction for atoms that are so close together, since their interaction should be able to be modelled adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, an interaction harmonic the O-O distance as a Urey-Bradley term). Thanks for Mark's suggestion. But I want to reproduce the simulation from the other paper, The paper describe the force-field that O-O nonbonded interaction in the same carbonate should be considered. In addition to that, I can't use buckingham potential in [pairs], even choose funct = 2. I am wondering if I want to describe 1-4 interaction by Buckingham, what could I do? This is one application for setting nrexcl for moleculetypes. You don't want exclusions for particles 2 bonds apart, so set this to one. See chapter 5. If that doesn't work, then if the bonded interactions are merely harmonic distance potentials, then GROMACS permits a form of them that doesn't create a bond (bond type 6, IIRC, check chapter 5; or constraint type 2). Thus, the automated exclusion mechanism won't be involved, and you can have Buckingham O-O so long as you have Buckingham for all other LJ interactions. You will need manual exclusions for C-O pairs, I guess. Thus [ atomtypes ] C #nonbonded parameters go here O #nonbonded parameters go here [moleculetype] carbonate [atoms] C O1 O2 O3 [bonds] C-O1 # type 6 C-O2 # type 6 C-O3 # type 6 [exclusions] 1 2 1 3 1 4 Whether this works may depend on whatever else is in your system, though. 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/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
[gmx-users] who can help me with the force-field?
Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] Re: who can help me with the force-field?
Mark wrote: xiao shijun wrote: Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! Usually you would not define a nonbonded interaction for atoms that are so close together, since their interaction should be able to be modelled adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, an interaction harmonic the O-O distance as a Urey-Bradley term). Thanks for Mark's suggestion. But I want to reproduce the simulation from the other paper, The paper describe the force-field that O-O nonbonded interaction in the same carbonate should be considered. In addition to that, I can't use buckingham potential in [pairs], even choose funct = 2. I am wondering if I want to describe 1-4 interaction by Buckingham, what could I do? BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] What can I to do with the problem: lincs warning and water can not be settled?
hi, The simulation was OK. But when I changed the epsilon of some atoms to get rid of LJ, lincs warning emerged as: step 116 ; time 0.232 LINCS warning ralative constraint deviation after LINCS: rms 0.168368, max 4.765960 (between atoms 858 and 856) bonds that rotated more than 30 degrees: t=0.232ps : water molecular starting at atom 17660 can not be settled. check for bad contact and/or reduce the timestep. then the warning happened every step untill the programm crashed. Thanks for your discussion!! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
