Re: [gmx-users] force field
Thanks for your email Justin. I remember you answered an email that there is a PRODRG server working with higher version of Gromos87. Could you show me the link please? Also could you please give me the advice about other force field for my simulation? I am working with surfactants like alcohols, CTAB and triton x45. Best regards, Van On 5 December 2012 20:00, Justin Lemkul jalem...@vt.edu wrote: On 12/4/12 10:22 PM, cuong nguyen wrote: Dear gmx users, i have got the coordinate and topol files of nonanol from the server: http://davapc1.bioch.dundee.**ac.uk/prodrg/submit.htmlhttp://davapc1.bioch.dundee.ac.uk/prodrg/submit.html the .gro file was download from option GROMOS87/GROMACS polar H's onlyhttp://davapc1.bioch.**dundee.ac.uk/cgi-bin/xprodrg#**DRGPOH.GROhttp://davapc1.bioch.dundee.ac.uk/cgi-bin/xprodrg#DRGPOH.GRO and .top file was from optionGROMACShttp://davapc1.**bioch.dundee.ac.uk/cgi-bin/** xprodrg#DRGGMX.ITPhttp://davapc1.bioch.dundee.ac.uk/cgi-bin/xprodrg#DRGGMX.ITP [D]http://davapc1.bioch.**dundee.ac.uk/cgi-bin/xprodrg/** 50BEBB0C5FDC78D6/asdl/**DRGGMX.ITPhttp://davapc1.bioch.dundee.ac.uk/cgi-bin/xprodrg/50BEBB0C5FDC78D6/asdl/DRGGMX.ITP (topology) Please let me know the name of this force field? GROMOS87/GROMACS indicates the GROMOS87 force field in GROMACS format. The GROMOS87 force field is deprecated, so you probably shouldn't be using it since far better parameter sets exist. Also note that PRODRG topologies are generally very inaccurate. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] force field
Dear Justin, with alcohols I can find their force field in AMBER or others. However, I have just got a paper regarding CTAB ( http://pubs.acs.org/doi/abs/10.1021/la302998k). They use Gromos force field. I am attempting to find the other better one. Best regards, Van On 6 December 2012 09:35, Justin Lemkul jalem...@vt.edu wrote: On 12/5/12 8:29 PM, cuong nguyen wrote: Thanks for your email Justin. I remember you answered an email that there is a PRODRG server working with higher version of Gromos87. Could you show me the link please? The server has changed and is now managed by a company. I have not used it in months; perhaps the interface has changed. One used to be able to select which force field to use. Also could you please give me the advice about other force field for my simulation? I am working with surfactants like alcohols, CTAB and triton x45. What does a search of the literature tell you? There are plenty of simulation papers regarding alcohols and surfactants. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Temperature Histogram
Dear, Thanks a lot for your suggestion Justin. I have a box 3 3 20 and want to plot the temperature along the z axis. I did the commands: g_energy -f NVT_20ns.edr -s topol.top -o temp g_analyze -f temp.xvg -dist temp.xvg and got the results: 281.9 0 282 0.000149997 282.1 0 282.2 0 282.3 0 282.4 0 282.5 0 282.6 0 282.7 0 282.8 0 282.9 0 283 0 283.1 0 283.2 0 283.3 0 283.4 0 283.5 0 283.6 0 283.7 0.000149997 283.8 0 283.9 0 284 0 284.1 0.000149997 284.2 0 284.3 0.000149997 . I supposed the first column should start from 0 to 20. Please tell me what's wrong I am doing? Best regards, Cuong On 8 November 2012 01:16, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 11:42 AM, Samadashvili Nino wrote: Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Use g_energy to extract temperatures from the .edr file, then g_analyze -dist on that .xvg file. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Lennard-Jones Parameters
Thanks for you email. I already had the .gro and .top files from PRODRG. Now I want to reproduce these files following the LJ parameters in a published paper (charge, sigma and epsilon values). I can change the charge in the top file, yet I do not know how to change sigma and epsilon values. Best regards, Cuong On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to reproduce the results of a published paper, you should use the forcefield and parameters specified in that paper and contact the author(s) if more details are needed. On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -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 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street 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 -- 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] Lennard-Jones Parameters
Dear, The top file downloaded from PRODRG did not consist of [atomtypes]. Please tell me how can I add and use this function? Best regards, Cuong On 15 October 2012 16:43, Peter C. Lai p...@uab.edu wrote: Is there no [atomtypes] section in the top file? On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote: Thanks for you email. I already had the .gro and .top files from PRODRG. Now I want to reproduce these files following the LJ parameters in a published paper (charge, sigma and epsilon values). I can change the charge in the top file, yet I do not know how to change sigma and epsilon values. Best regards, Cuong On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to reproduce the results of a published paper, you should use the forcefield and parameters specified in that paper and contact the author(s) if more details are needed. On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -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 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street 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 -- 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
Re: [gmx-users] Lennard-Jones Parameters
Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
[gmx-users] mdrun-gpu
Dear Gromacs Users, I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support. when I run grompp-gpu to generate the .tpr file, it worked well: grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96 however, then I run mdrun-gpu mdrun-gpu -s min -o min -c min.g96 -x min -e min -g min, it was stopped with the error: Fatal error: OpenMM supports only the following integrators: md/md-vv/md-vv-avek, sd/sd1, and bd. Could someone please explain what this error means and the appropriate way to remedy it? Thank you in advance. Best regards, Cuong -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] genconf command
Dear Gmx-users, I created a box size 4 4 2 and named layer.gro. Then genconf was used to doulble this box: genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8 However, the copied box has the same direction as the original box. Could you please help me to rotate 180 degrees the copied one? Thank you very much. Best regards, Cuong -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Calculate surface tension
Dear Gromacs Users, I am trying to calculate the surface tension at air/water interface of water model SPC/E. I used the command g_energy and chose #surfacetension. However, the output file was like this: 0 14001.49219 0.5 21139.67773 1 7328.798828 1.5 16114.55664 2 8224.392578 2.5 16558.38867 3 8603.480469 3.5 -8019.197754 4 -8756.329102 4.5 4309.573242 5 5473.54541 5.5 -4476.996094 6 -2218.013672 6.5 -8038.819336 7 8374.514648 7.5 10971.41602 8 9115.582031 Please let me know how to deal with this result to get the surface tension value as reported in some articles? Thank you in advance. Regards, Cuong -- 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] Index selection in g_potential
Hi, if you want to calculate the potential of some groups (0, 3, 11), using make_ndx to creat a new group consisting of these groups. Then running g_potential. Cuong 2012/5/16 Andrew DeYoung adeyo...@andrew.cmu.edu Hi, I am using the utility g_potential. It takes (among other files) an index file. At the beginning of the run, it prompts me for a selection from the index file. Is it possible to make more than one selection, such that the potential is calculated for each selection, _separately_? If I enter something like this: 0 3 11 The output seems to only include the potential due to the first selection (0) and seems to ignore the others. Thanks for your time! Andrew DeYoung Carnegie Mellon University -- 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 -- 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
[gmx-users] Getting local pressure
Dear, Could anyone please let me know, in Gromacs analysis is there any way to get the local pressure (along z-axis of the box)? Thanks a lot! Cuong Nguyen -- 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
[gmx-users] Box of water
Dear Gromacs Users, I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10 to create box of 3010 water molecules. However, now I need to create a same size box with only 846 water molecules. Please help me to do this. Thanks, Cuong -- 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] Box of water
Thanks, I tried to add -maxsol 846 to the command and got the box with 846 water molecules. However, when I use VMD to visualize the box, these molecules concentrate on 1/3 the box space. I do need the molecules to spread out whole box. Cheers, Cuong 2012/5/1 Justin A. Lemkul jalem...@vt.edu On 4/30/12 10:02 PM, cuong nguyen wrote: Dear Gromacs Users, I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10 to create box of 3010 water molecules. However, now I need to create a same size box with only 846 water molecules. Please help me to do this. Use the -maxsol option when invoking genbox. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] mpirun
Dear Gromacs Users, as in the manual, I tried to run the simulation on 4 processors and used the command as follow: *mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x NVT_50ns -e NVT_50ns -g NVT_50ns -v* Then I got the error: *mpirun was unable to launch the specified application as it could not find an executable: Executable: mdrun_mpi* Please help me to deal with this problem. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] using MPI
Thanks Erik, In case I run my simulations on 4 nodes, please let me know what do I have to add to the command to start MPI? I have used the commands: *grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g NVT_50ns -v* however, the speed was still the same. Best regards, Cuong 2012/3/15 Erik Marklund er...@xray.bmc.uu.se If you are to run on a single node, then there's no need for mpi nowadays. mdrun uses all cores it can find anyway. If you need to split your calculation over many machines, however, you will need mpi. Best, Erik 15 mar 2012 kl. 04.50 skrev cuong nguyen: Dear Gromacs users, I prepare to run my simulations on the supercomputer on single node with 64 CPUs. Although I have seen on Gromacs Mannual suggesting to use MPI to parellel, I still haven't understood how to use this application and which commands I have to use. Please help me to deal with this? Many thanks and regards, Cuong -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] genbox
You can use the command genbox -cs with the option -maxsol number to specify the number of water molecules Good luck Cuong 2012/1/16 vidhya sankar scvsankar_...@yahoo.com Hello Justin, Thanks for your patient reply I would like to solvate my molecules with specific number of water molecules what option is a suitable to do that ? in editconf with regards S.Vidhya sankar -- 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 -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users]-Snapshots
Dear Users, Please let me know if we can get snapshot from GROMACS. I am using version 4.4. Thanks and best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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]-Snapshots
Thanks a lot Justin. I have just used trjconv -dump with the command trjconv -s NVT_final2ns.tpr -f NVT_final2ns -o trjconv.gro -dump 1 to extract a frame. However, I still do not know how to get the snapshot like a 3D picture . Please help me! Many thanks Cuong Nguyen 2012/1/10 Justin A. Lemkul jalem...@vt.edu cuong nguyen wrote: Dear Users, Please let me know if we can get snapshot from GROMACS. I am using version 4.4. The final configuration of any simulation is written to a coordinate file by default. You can extract any frame from your trajectory using trjconv -dump. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] CTAB force field
Dear all, I prepare to do simulation about the solution of CTAB. Does anyone know the force field (top and gro files) of CTAB which were published before? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] No such moleculetype Na
Hi Setare, You should find the ions.itp file in your computer, open and see the exact name of sodium in this file. Use this name when using the command genion. Good luck! Cuong 2011/12/10 Setare Jiji jj.64fh...@yahoo.com Hi, I am running Tutorial 1: Lysozyme in Waterhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html . I used 4-0-7 version and the sequence is true but in minimization energy step,I have this fatal error: No such moleculetype Na so,what do I do? Best regards -- 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 -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] itp file for D2O
Dear GROMACS users, I usually use spce.itp file for water solvent in my simulation. However, now I want to change this solvent to deuterium monoxide (D2O). Please let me know if I have to change this itp file? if yes, where can I find this file? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] how to know the pH of a solution
Dear, I have made a 10x10x10 box with 200 hexanoic acid molecules and fill full of water. Please let me know how can I do to know and change the pH of this solution? Thank you very much. Cheers, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] Adding ions using genion
Dear, I create a box of water with 10 MIBC molecules on two opposite surfaces. then I used the command grompp -f input_min.mdp -o min.tpr -c box1.g96 to creat .tpr file before using the command genion -s min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20 to add 20 Na+ and 20 Cl- into this box. I run the command grompp -f input_min.mdp -o min.tpr -c add.gro again and appeared the warings : Warning: atom name 176 in topol.top and add.gro does not match (CL - OW) Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1) Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2) Warning: atom name 179 in topol.top and add.gro does not match (CL - OW) Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 72]: 21754 non-matching atom names atom names from topol.top will be used atom names from add.gro will be ignored .. Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. then I tried with the command grompp -f input_min.mdp -o min.tpr -c add.gro -maxwarn 2000 and it run well. However, when I kept working with the command mdrun -s min -o min -c min.g96 -x min -e min -g min, the errors appeared as follow: Fatal error: 3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me to fix this problem. Many thanks. Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] Create gro and top file for hexanoic acid
Dear Sir/Madam, I have tried to creat the gro and top file for acid hexanoic by using the PRODRG server. However, the atom H in -COOH group could not be found and two O atoms are the same. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DRG OAB 1 -0.767 15.9994 2 C 1 DRG CAI 10.343 12.0110 3OM 1 DRG OAC 1 -0.766 15.9994 4 CH2 1 DRG CAH 10.048 14.0270 5 CH2 1 DRG CAG 10.047 14.0270 6 CH2 1 DRG CAF 10.047 14.0270 7 CH2 1 DRG CAE 10.048 14.0270 8 CH2 1 DRG CAD 20.000 14.0270 9 CH3 1 DRG CAA 30.000 15.0350 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.125 1340.00.125 1340.0 ; CAI OAB 2 3 20.125 1340.00.125 1340.0 ; CAI OAC 2 4 20.153 715.00.153 715.0 ; CAI CAH 4 5 20.153 715.00.153 715.0 ; CAH CAG 5 6 20.153 715.00.153 715.0 ; CAG CAF 6 7 20.153 715.00.153 715.0 ; CAF CAE 7 8 20.153 715.00.153 715.0 ; CAE CAD 8 9 20.153 715.00.153 715.0 ; CAD CAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; OAB CAG 2 6 1 ; CAI CAF 3 5 1 ; OAC CAG 4 7 1 ; CAH CAE 5 8 1 ; CAG CAD 6 9 1 ; CAF CAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2126.0 770.0126.0 770.0 ; OAB CAI OAC 1 2 4 2117.0 635.0117.0 635.0 ; OAB CAI CAH 3 2 4 2117.0 635.0117.0 635.0 ; OAC CAI CAH 2 4 5 2109.5 520.0109.5 520.0 ; CAI CAH CAG 4 5 6 2109.5 520.0109.5 520.0 ; CAH CAG CAF 5 6 7 2109.5 520.0109.5 520.0 ; CAG CAF CAE 6 7 8 2109.5 520.0109.5 520.0 ; CAF CAE CAD 7 8 9 2109.5 520.0109.5 520.0 ; CAE CAD CAA [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 0.0 167.40.0 167.4 ; imp CAI OAB OAC CAH 5 4 2 1 1 0.01.0 6 0.01.0 6 ; dih CAG CAH CAI OAB 6 5 4 2 1 0.05.9 3 0.05.9 3 ; dih CAF CAG CAH CAI 7 6 5 4 1 0.05.9 3 0.05.9 3 ; dih CAE CAF CAG CAH 8 7 6 5 1 0.05.9 3 0.05.9 3 ; dih CAD CAE CAF CAG 9 8 7 6 1 0.05.9 3 0.05.9 3 ; dih CAA CAD CAE CAF Please help me to correct this mistake. Many thanks. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology -- 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] how to make topol.top file for mixed solution
Dear, I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands: *genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top* then I filled this mixture by water to create other 5 5 10 box by using comands: *genbox -cp mix.gro -cs spc216.gro -o box1.g96 -p topol.top -box 5 5 10* the topol.top file is: *#include ffG43a1.itp #include decanol.itp #include mibc.itp ; include water #include spce.itp [ system ] MIBC and dec in water [ molecules ] dec 15 mibc 15 sol 7947.* then I ran the grompp comand: grompp -f input_min.mdp -o min.tpr -c box1.g96 and the errors was *Warning: atom name 2 in topol.top and box1.g96 does not match (CAC - CAF)* *Warning: atom name 3 in topol.top and box1.g96 does not match (CAE - CAB)* *Warning: atom name 4 in topol.top and box1.g96 does not match (CAG - CAE)* *Warning: atom name 5 in topol.top and box1.g96 does not match (CAI - CAG)* *Warning: atom name 6 in topol.top and box1.g96 does not match (CAK - CAC)* *Warning: atom name 7 in topol.top and box1.g96 does not match (CAJ - OAD)* *Warning: atom name 8 in topol.top and box1.g96 does not match (CAH - HAN)* *Warning: atom name 9 in topol.top and box1.g96 does not match (CAF - CAA)* *Warning: atom name 10 in topol.top and box1.g96 does not match (CAD - CAF)* *WARNING 1 [file topol.top, line 20]:* * 220 non-matching atom names* * atom names from topol.top will be used* * atom names from box1.g96 will be ignored* *--- * *Fatal error:* *Too many warnings (2), grompp terminated.* *If you are sure all warnings are harmless, use the -maxwarn option.* *For more information and tips for troubleshooting, please check the GROMACS * *website at http://www.gromacs.org/Documentation/Errors * Please help me to correct these errors. Thank you very much best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu cuong nguyen wrote: Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to create a suitable topol.top file to this system. No one can help you without knowing the exact errors that grompp produced. -Justin Thanks a lot. Best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Justin A. Lemkul wrote: cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please read the tutorial: http://www.gromacs.org/__**Documentation/Tutorials#__** Heterogeneous_Systemshttp://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems http://www.gromacs.org/**Documentation/Tutorials#** Heterogeneous_Systemshttp://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems Also possibly useful: http://www.gromacs.org/__**Documentation/How-tos/Mixed___**Solventshttp://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents http://www.gromacs.org/**Documentation/How-tos/Mixed_**Solventshttp://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http
Re: [gmx-users] Regarding Table Extension
Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please help me. Thank you very much. Best regards, Cuong 2011/11/7 Dallas Warren dallas.war...@monash.edu Might I suggest you actually state what you don’t understand. Otherwise you are leaving an open ended question for people to respond to, which they are unlikely to do so. The more specific and more detail you put into your question, the more likely you are to get some useful assistance. ** ** “table-extension = 20 ; (nm) !IMPORTANT! Set this so that rvdw + table-extension equals half of the box's longest diagonal.” ** ** Are you aware of the situation to which that sample .mdp file is used? Is that situation applicable for what you are doing? ** ** Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Ravi Kumar Venkatraman *Sent:* Saturday, 5 November 2011 8:13 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Regarding Table Extension ** ** *Dear All, This is the site where they have mentioned like the sum of the longest diagnol of the box + rlist = table extension http://smog.ucsd.edu/MDP_sample.html Further whatever that was mentioned in the manual I could not understand. I kindly request any one of you to explain me the same. Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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 -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] how to make topol.top file for mixed solution
Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please help me. Thank you very much. Best regards, Cuong Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] how to make topol.top file for mixed solution
Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to create a suitable topol.top file to this system. Thanks a lot. Best regards, Cuong 2011/11/7 Justin A. Lemkul jalem...@vt.edu Justin A. Lemkul wrote: cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please read the tutorial: http://www.gromacs.org/**Documentation/Tutorials#**Heterogeneous_Systemshttp://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems Also possibly useful: http://www.gromacs.org/**Documentation/How-tos/Mixed_**Solventshttp://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] Gromacs inquiries
Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top. However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the number 10 in the instruction to 1000 or 1, it will run well but I do not know if this box is full. Please help me to change this instruction. Thanks a lot. Regards, Cuong 2011/10/26 Mark Abraham mark.abra...@anu.edu.au On 26/10/2011 1:46 PM, cuong nguyen wrote: Dear, Thanks a lot for useful software. I am trying to generate a box (4 4 4) with full hexanol molecules inside. I have used the instruction genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top, however it has not been successful. Unfortunately we can't help if we don't know what is in your -ci box (also, it's probably best not to use capitalized filename extensions), or why you think the procedure was not successful. Please consider the advice here http://www.gromacs.org/Support**. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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
[gmx-users] Gromacs inquiries
Dear, Thanks a lot for useful software. I am trying to generate a box (4 4 4) with full hexanol molecules inside. I have used the instruction genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top, however it has not been successful. Please correct the instruction for me or give me any advice. Best regards, Cuong -- 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
