Re: [gmx-users] tcoupling

Hi, I haven't really checked how it is with the new version (and you're not telling which version you're using anyway), but grompp used to get confused with multiple molecules and only report the charge on one of them. You can check the total charge from the .tpr file with (bash command line): gm

Re: [gmx-users] tcoupling

shahrbanoo karbalaee wrote: Dear justin ok.you areright.if I add another cl- ,it will negative than more.I know my peptide of charge is +1.please tell me no problem if with warning continue. I'm not clear which warning you're referring to. If you're being told you have a non-zero charge,

[gmx-users] tcoupling

Dear justin ok.you areright.if I add another cl- ,it will negative than more.I know my peptide of charge is +1.please tell me no problem if with warning continue. --best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs

Re: [gmx-users] tcoupling error

shahrbanoo karbalaee wrote: Dear thanks for your answer. I did as you tell me about usingcapital letter .about charge I guess it related to tfe and protonated amino acid.after change it I still have this warning. Then it's not case sensitivity, but what Mark told you is still

[gmx-users] tcoupling error

Dear thanks for your answer. I did as you tell me about usingcapital letter .about charge I guess it related to tfe and protonated amino acid.after change it I still have this warning. best -- sh-karbalaee ___ gmx-users mailing listg

Re: [gmx-users] tcoupling

Mark Abraham wrote: shahrbanoo karbalaee wrote: hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Exclu

Re: [gmx-users] tcoupling

shahrbanoo karbalaee wrote: hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbour

[gmx-users] tcoupling

hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 turning all