Re: [gmx-users] combination rules -- the part aboutthecombinationrules

other atoms as well, you will need to find a consistent force field, probably or completely LJ or completely Buckingham. Berk Date: Thu, 26 Feb 2009 09:22:26 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] combination rules -- the part

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

Shuangxing Dai wrote: Thank you for your help. I checked all the force field, all of them are with default non-bond params in LJ. So I still need to try new solution. I add my non bond parameters in the .top file generated. Force field files were not changed. Then I use grompp, the error was:

RE: [gmx-users] combination rules -- the part aboutthecombinationrules

From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] combination rules -- the part aboutthecombinationrules Shuangxing Dai wrote: Yes, add parameters for crystalline zinc oxide, which require Buckingham nonbonded interactions, that is what I am doing. I think

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

Yes, add parameters for crystalline zinc oxide, which require Buckingham nonbonded interactions, that is what I am doing. I think I have changed all the necessary parts for the Buckingham potential. Is there any direct way to accomplish my goal? Since in ffgmxnb.itp, all the nonbond_params are LJ

Re: [gmx-users] combination rules -- the part aboutthe combinationrules

Sent: Friday, February 20, 2009 6:02 PM Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules Shuangxing Dai wrote: Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; ij func abc6 Zn O2

RE: [gmx-users] combination rules -- the part aboutthe combinationrules

Hi, Is line 68 one of the lines you have added, or another one? Berk From: shuangxing...@gmail.com To: gmx-users@gromacs.org Subject: Re: [gmx-users] combination rules -- the partaboutthe combinationrules Date: Sun, 22 Feb 2009 14:55:21 -0700 Thank you. I have referred

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

for GROMACS users Sent: Sunday, February 22, 2009 3:03 PM Subject: RE: [gmx-users] combination rules -- the part aboutthecombinationrules Hi, Is line 68 one of the lines you have added, or another one? Berk From: shuangxing...@gmail.com To: gmx-users@gromacs.org Subject: Re

Re: [gmx-users] combination rules -- the part aboutthecombinationrules

Shuangxing Dai wrote: No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines of error informaion like this: ERROR 77 [file ffgmxnb.itp, line 144]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) Sure, this is predictable. This force field's files

Re: [gmx-users] combination rules -- the part about the combinationrules

, February 18, 2009 11:39 AM Subject: RE: [gmx-users] combination rules -- the part about the combinationrules Hi, No pairtypes are for bonded pair interactions, not for combinations of non-bonded interactions. The manual tells you how to do this: [ nonbond_params ] A_ii A_jj 2 a b

Re: [gmx-users] combination rules -- the part about the combinationrules

Shuangxing Dai wrote: Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; ij func abc6 Zn O2 ... . But error occured.. ERROR 1 [file ffgmxnb.itp, line 270]: Trying to add Buck.ham (SR) while the default

[gmx-users] combination rules

Hello, I was wondering how to set up parameters for interactions between two different atoms A and B. Since for Gromacs parameters are defined to each kind of atom, I cannot specify parameters between A and B. For Buckingham potential, the rule was: A_ij=(A_ii * A_jj)^(1/2) So anyone

Re: [gmx-users] combination rules

Shuangxing Dai wrote: snip I also have problem in installing xmgr. I use MacOSX 10.5.5. I type ./configure and got this error messege: ecme222-96-dhcp:xmgr-4.1.2 ssx$ ./configure creating cache ./config.cache checking host system type... configure: error: can not guess host type; you must

[gmx-users] combination rules -- the part about the combination rules

For LJ interactions, use [ pairtypes ]. For Coulombics there is unfortunately no analogous solution. I am not clear about exactly what you want to do. What parameters are you interested in, or by this do you just mean LJ and Q? Chris. -- original message -- Hello, I was wondering how

RE: [gmx-users] combination rules -- the part about the combination rules

: [gmx-users] combination rules -- the part about the combination rules For LJ interactions, use [ pairtypes ]. For Coulombics there is unfortunately no analogous solution. I am not clear about exactly what you want to do. What parameters are you interested in, or by this do you just

Re: [gmx-users] combination rules

Dear Mark, Thanx for your reply. Chapter 5 describes it, but I guess that is described in a more general way! GORMOS87 uses a different kind of scaling which is not mentioned in chapter 5 and hence I am just curious to know whether GROMOS96 also uses same scaling scheme as is used for GROMOS87

Re: [gmx-users] combination rules

priyanka srivastava wrote: Dear Mark, Thanx for your reply. Chapter 5 describes it, but I guess that is described in a more general way! GORMOS87 uses a different kind of scaling which is not mentioned in chapter 5 and hence I am just curious to know whether GROMOS96 also uses same scaling

[gmx-users] combination rules

Dear All, I would be really thankful if somebody could tell me the combination rules used for creating the [pairtypes] in lipid.itp (i.e. the 1,4 interactions) in GROMOS96. Is it the same as is used in GROMOS87? eagerly waiting for the reply, regards, Pri...