Re: [gmx-users] Hi All..one question about charge making
uki zhu wrote: Dear all gmx-users, Sorry to bother you. I am trying to make a molecule with a unit charge well-distributed. But I do not know how to write such *.top file. Does every atom get the same charge at the beginning? And can we use Gromacs to simulate the changes of the charge distribution? I don't understand what you're trying to do, or why you think GROMACS is suited for doing it. Mark ___ 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
[gmx-users] Hi All..one question about charge making
Dear all gmx-users, Sorry to bother you. I am trying to make a molecule with a unit charge well-distributed. But I do not know how to write such *.top file. Does every atom get the same charge at the beginning? And can we use Gromacs to simulate the changes of the charge distribution? Any help would be appreciated! Thank you very much! Regards, UKI ___ 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
[gmx-users] Hi All
Nice to meet you. ___ 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] Hi all
ann rose wrote: Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? Yes - this information is part of the force field. If so how can I incoroprate this into gromacs? You will need a thorough working knowledge of at least chapter 5 of the manual, and plenty from earlier sections. This will also let you assess whether the range of functions computed by gromacs is suitable for your forcefield. and also How to get the starting configuration for the poysiloxanes? ( like .gro, .top, .itp files) .gro files are structure files... you're responsible for generating them. Search the mailing list for suggestions. .top files can be generated by pdb2gmx if you can generate suitable .rtp monomers, but life may be messy here for branched polymers... you may need to make these by hand. .itp files are included by .top files and include your basic force field files as well as regularly recycled units like solvents... you need to make these. Mark ___ 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
[gmx-users] Hi all
Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? If so how can I incoroprate this into gromacs? and also How to get the starting configuration for the poysiloxanes? ( like .gro, .top, .itp files) Thanking you in advance ann ___ 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] Hi all!
Marcelo Fabricio Masman wrote: Hi all!!! I am using the programme grompp (double precision) and the programme genion to make "neutral" .top and .tpr files. But after change the quantity of H2O molecules and add the line with the necessary Na+ ions I am still having WARNING and the charge is STILL negative. What happend? What am I doing wrong? Should I do something else? Here are the WARNING banners: Generated 243951 of the 243951 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 41338 WARNING 1 [file "Ab-1.top", line 5860]: Too few parameters on line (source file toppush.c, line 1096) Excluding 2 bonded neighbours for 3 Na+ WARNING 2 [file "Ab-1.top", line 5860]: System has non-zero total charge: -3.00e+00 processing coordinates... WARNING 3 [file "Ab-1.top", line 5860]: Bad box in file Ab-1_n.gro you have the wrong order of things in your topology file and you haven't updated the number of atoms in the gro file (should be 6 fewer) Generated a cubic box 10.898 x 10.838 x 10.922 double-checking input for internal consistency... renumbering atomtypes... Thank you very much. Marcelo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, Assoc. Prof., Molecular Biophysics group, 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 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
[gmx-users] Hi all!
Hi all!!! I am using the programme grompp (double precision) and the programme genion to make "neutral" .top and .tpr files. But after change the quantity of H2O molecules and add the line with the necessary Na+ ions I am still having WARNING and the charge is STILL negative. What happend? What am I doing wrong? Should I do something else? Here are the WARNING banners: Generated 243951 of the 243951 1-4 parameter combinationsExcluding 3 bonded neighbours for Protein_A 1Excluding 2 bonded neighbours for SOL 41338WARNING 1 [file "Ab-1.top", line 5860]: Too few parameters on line (source file toppush.c, line 1096)Excluding 2 bonded neighbours for 3 Na+WARNING 2 [file "Ab-1.top", line 5860]: System has non-zero total charge: -3.00e+00 processing coordinates...WARNING 3 [file "Ab-1.top", line 5860]: Bad box in file Ab-1_n.groGenerated a cubic box 10.898 x 10.838 x 10.922double-checking input for internal consistency... renumbering atomtypes... Thank you very much. Marcelo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
