[gmx-users] How to define the center of mass for a droplet consisting of different ions and molecules?
Dear all,I would like to construct a code to describe the center of mass of a droplet, with water and ions.For the following GROMACS trajectory file (confout.gro), we can have water coordinates as: 57SOL OW 36289 17.563 14.835 0.520 57SOL HW1 36290 17.602 14.916 0.487 57SOL HW2 36291 17.571 14.843 0.615 58SOL OW 36292 17.588 14.547 0.457 58SOL HW1 36293 17.573 14.642 0.458 58SOL HW2 36294 17.521 14.512 0.516 59SOL OW 36295 11.747 17.611 1.159 59SOL HW1 36296 11.714 17.522 1.174 59SOL HW2 36297 11.740 17.624 1.064To describe the center of mass of each molecule, we can have the following for-loop:for i = 1:length(x)/3 xcm(i) = (x(i*3-2)*massO + x(i*3-1)*massH + x(i*3)*massH)/massWater; ycm(i) =(y(i*3-2)*massO + y(i*3-1)*massH + y(i*3)*massH)/massWater; zcm(i) =(z(i*3-2)*massO + z(i*3-1)*massH + z(i*3)*massH)/massWater;endThen, the center of mass of a droplet (100% water) can be defined by:cmx = sum(xcm)/length(x)*3;cmy =sum(ycm)/length(y)*3;cmz =sum(zcm)/length(z)*3;For a droplet consisting of H2O, H3O, and Chloride ions, how does one describe the center of mass of each molecule/ion using the for-loop, and then using the xcm(i), ycm(i), and zcm(i) to determine the center of the droplet?Below is an example of the coordinate file:2015SOL OW 42163 17.143 16.975 0.5022015SOL HW1 42164 17.175 17.038 0.5672015SOL HW2 42165 17.222 16.937 0.4642016SOL OW 42166 16.088 17.097 0.7782016SOL HW1 42167 16.094 17.182 0.7342016SOL HW2 42168 16.159 17.098 0.843. . . 2035H3O OW 42241 17.895 20.054 0.5612035H3O H31 42242 17.836 20.100 0.4922035H3O H32 42243 17.970 20.114 0.5932035H3O H33 42244 17.930 19.964 0.5272036H3O OW 42245 13.948 17.327 0.5032036H3O H31 42246 13.875 17.348 0.5712036H3O H32 42247 13.978 17.410 0.4522036H3O H33 42248 14.026 17.276 0.544. . . 2037CLA CL 42249 13.862 17.882 1.7542038CLA CL 42250 16.686 17.457 0.667Thanks in advance.Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding polyatomic species in water
Check whether the configuration of the atom with highest force is configured reasonably.If you are only getting a few minimisation steps before crashing, then perhaps minimising your cell using a double precision GROMACS would help?Cheers,Kester- 원본 메일 -보낸사람 : #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg받는사람 : "gmx-us...@gromacs.org" gmx-us...@gromacs.org받은날짜 : 2015년 2월 4일(수) 19:10:26제목 : [gmx-users] adding polyatomic species in waterDear Gromacs Users, I am trying to simulate a cell containing different polyatomic species like sulphate, glucose, acetic acid etc. in water. I start my simulation by taking pdb file containing 1 sulphate ion and then add remaining sulphate ions and other species using -cs and -ci from genbox. I use genbox command multiple time till all the species are added and system is solvated in water. But when I perform energy minimisation, the initial system starts with a very high energy i.e. around 10^6 range and the either it doesn't get converged or i get msg Segmentation fault (core dumped). I also tried using genconf but still i was getting the same problem. Can anyone please let me know what is wrong with my system and how can i correctly add all the species in my system. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to g_select water and ions?
Dear all,I would like to select water and ions using the g_select command as follows:g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 1 -select 'resname SOL and resname H3O and resname CLA and res_com z = 0.8 and res_com z 0.85' -on Layer-001.ndx In my ions.itp file, I have my hydronium and chloride as H3O and CLA, however, I am not able to obtain the select-index file.However, selecting water without ions worked, but this is not what I wanted.Could anyone point out what did I do incorrectly?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF plot with large g(r) values
Hi Andre,Thank you for your input.보낸사람 : "André Farias de Moura" mo...@ufscar.br받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2015년 1월 8일(목) 22:05:39제목 : Re: [gmx-users] RDF plot with large g(r) valuesRDF values are sensitive to the volume of the system, so if you put the same solutes inside a larger/smaller box, RDF values change accordingly (check basic definitions of RDF in simulation handbooks to make sure you understand this relation).Ah right, that explains why my RDF values dropped if I put a larger amount of water in the same box. and even if you have the same size and composition, RDF may become really large if molecules aggregate.Yep, I have a droplet where the Na+ and OH- ions tend to aggregate within the solution, the high g(r) peak in the RDF almost doubles the other systems with no aggregation.In this case, can I still use my RDF plots?Regards,Kester On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. The x-axis (nm), however, seemed to be correct. Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF plot with large g(r) values
Dear Justin, No, I am not comparing equivalent systems, nor reproducing previous findings. My simulation box contains a droplet of 2000 water molecules on graphene.The RDF of g(r) Ow-Ow shows a first peak at r = 0.3 nm, with a peak height of 400.For 6000 and 10,000 water molecules, the peak heights are 200 and 100, respectively. Is this due to the large vacuum in my simulation box?Regards,KesterOn 1/8/15 4:48 AM, Kester Wong wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12. Are you comparing equivalent systems, e.g. trying to reproduce previous findings? If not, it's just apples and oranges. Your result is not necessarily unusual. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to plot a droplet radius profile as a function of z-directio
Dear Justin and all,보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 12월 27일(토) 23:55:33제목 : Re: [gmx-users] How to plot a droplet radius profile as a function of z-directio On 12/27/14 2:05 AM, Kester Wong wrote: Dear gmx-users, Q1) I would like to plot the radius profile of a water droplet on graphene, as a function of z-direction, as per below: http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/large Which GROAMCS utility should I use, and how do I go about plotting the profile? It will require several steps. Not something I've ever done, but I would think g_traj for coordinate extraction, then post-processing to calculate the diameter or radius, would be the first step. Presumably you would have to do this for various slices (assuming you're looking at cross-sections in the x-y plane for varying values of z), so g_select to define atoms within that slice will be needed before even running g_traj. Then you construct the profile from this information. I have selected the slices of water along the z-direction. I assume the next step would be using g_traj to extract the coordinates.How do I go from running g_traj to post-processing the droplet radius?Do I use this command as follows:g_traj -f traj_comp.xtc -s topol.tpr -n selected-bins.ndx -b 9000 -e 1 -nojump -fp -ox coord.xvg Regards,Kester Q2) Another question that I have is, suppose I have equilibrated (NVT) a water droplet for 10ns, and would like to plot the H-bond density (along the z-direction), I type the following command: g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 1 -sl 1000 -dens number -o number-density-OH.xvg I was only able to select: System Graphene (my substrate) Water How can I create a system.ndx such that it allows me to choose the OH (instead of water)? make_ndx or g_select create index files. If you're defining "hydrogen bond density" as "number of hydrogen bonds per slice," along with the above, you need g_select and then you need g_hbond. g_density is not the right program here. Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the time frame of 9 - 10 ns, but does it average the frames to give a time-averaged density.xvg? Yes. But again, g_density is probably not what you want here; see the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1
Hi Teemu and all,Thank you for your reply email.보낸사람 : Teemu Murtola teemu.murt...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2015년 1월 2일(금) 01:15:25제목 : Re: [gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1Hi, Please check the manual for the version you're using, or preferably for the latest patch release, in case some things have been improved. The short section on selections in the manual (can't check the section number right now) mentions two different ways to access the help, and -select 'help ...' is not one of them. You can try, e.g., 'gmx help selections'.The command "gmx_mpi help selections" did show the available subtopics, however I find this paragraph confusing:To get started with selections, run, e.g., gmx_mpi select without specifyingselections on the command-line and use the interactive prompt to try outdifferent selections. This tool provides output options that allow one to seewhat is actually selected by the given selections, and the interactive promptreports syntax errors immediately, allowing one to try again. The subtopicslisted below give more details on different aspects of selections.Although the paragraph above mentioened "gmx_mpi select without specifying selections", I had to use "gmx_mpi help selections positions" to be able to see the thread "SPECIFYING POSITIONS IN SELECTIONS". The support for help through non-interactive selections like in -select 'help' was removed for 5.0 for a few different reasons. The main one is that 'gmx help' provides a much more natural way to access the information, in particular now that there are several different command line options that accept selections (for example, 'gmx gangle' has two different options that accept selections, and it's not exactly intuitive that these would/should also accept requests for generic selection help). It's an unfortunate coincidence that "help all" is now parsed as a valid selection (that has the name "help" and selects all atoms).Yep, I see. I can understand how this could be counter-intuitive. I got a little confused too, using g_select -h and gmx help selections. For your second question, is there something wrong with just extending your existing selection with an additional clause, for example like this: "resname SOL and res_com z = 10 and res_com z 15"? Yep, this worked for my systems.I suppose this binning method has already taken into account the center of mass of the water droplet?How do I go from here, to producing the water density profile as a function of z-direction?Best regards,KesterBest regards, Teemu On Jan 1, 2015 5:49 AM, "Kester Wong" <kester2...@ibs.re.kr> wrote: Dear all, I have recently posted a question on how generate data that allows me to plot a droplet profile as a function of z-direction. https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg08966.html Knowing that this procedure requires the use of g_select, I am able to look up some old posts on gmx-users mail list, however, typing g_select -select 'help position' and g_select -select 'help all' simply won't work (single quotation used instead of double quatation). I have tried these commands on GROMACS (5.0 single and 5.0.1 double precision). Also, I have another specific question on binning my water droplet along the z-direction: Firstly, I am only able to use g_select to define the bottom bin for water droplet; could you please advise on indexing the bins from the bottom water layer? g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 1 -select 'resname SOL and res_com z 10' -on output-system.ndx How does one select SOL between z 10 and z 15, so on and so forth? Happy New Year, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to plot a droplet radius profile as a function of z-directio
Dear Justin and all,I am stoked by what g_select can do (after reading the gmx-users list) and there is no one-size-fits-all.However, as I wanted to look for more resources on g_select, I was met with no further information, for example:g_select_mpi -select 'help position' OR g_select_mpi -select 'help all'The commands below did not return anything but "No trajectory or topology provided, nothing to do!".On 12/27/14 2:05 AM, Kester Wong wrote: Dear gmx-users, Q1) I would like to plot the radius profile of a water droplet on graphene, as a function of z-direction, as per below: http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/large Which GROAMCS utility should I use, and how do I go about plotting the profile? It will require several steps. Not something I've ever done, but I would think g_traj for coordinate extraction, then post-processing to calculate the diameter or radius, would be the first step. Presumably you would have to do this for various slices (assuming you're looking at cross-sections in the x-y plane for varying values of z), so g_select to define atoms within that slice will be needed before even running g_traj. Then you construct the profile from this information. Firstly, I am only able to use g_select to define the bottom bin for water droplet; could you please advise on indexing the bins from the bottom water layer?g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 1 -select 'resname SOL and res_com z 10' -on output-system.ndxHow does one select SOL between z 10 and z 15, so on and so forth? I have looked at this for reference:https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-June/072150.htmlI am aware that after g_select, I will also have to do the following- Perform center of mass calc to identify the relative position of the droplet: g_traj -f traj_comp.xtc -s topol.tpr -n system.ndx -com -fp -b 9000 -e 1 -ox coord.xvg- Suppose there are more than one frame within the 9-10ns period, a shell script will be needed to loop through the frames for the (R,z) extraction?One must then use a shell script to conduct further analysis using the produced index files, something like your script below?https://www.mail-archive.com/gmx-users@gromacs.org/msg52656.htmlThanks for your advise and I wish you ajolly2015!Regards,Kester Q2) Another question that I have is, suppose I have equilibrated (NVT) a water droplet for 10ns, and would like to plot the H-bond density (along the z-direction), I type the following command: g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 1 -sl 1000 -dens number -o number-density-OH.xvg I was only able to select: System Graphene (my substrate) Water How can I create a system.ndx such that it allows me to choose the OH (instead of water)? make_ndx or g_select create index files. If you're defining "hydrogen bond density" as "number of hydrogen bonds per slice," along with the above, you need g_select and then you need g_hbond. g_density is not the right program here. Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the time frame of 9 - 10 ns, but does it average the frames to give a time-averaged density.xvg? Yes. But again, g_density is probably not what you want here; see the help description. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1
Dear all,I have recently posted a question on how generate data that allows me to plot a droplet profile as a function of z-direction.https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg08966.htmlKnowing that this procedure requires the use of g_select, I am able to look up some old posts on gmx-users mail list, however, typing g_select -select 'help position' and g_select -select 'help all' simply won't work (single quotation used instead of double quatation).I have tried these commands on GROMACS (5.0 single and 5.0.1 double precision).Also, I have another specific question on binning my water droplet along the z-direction:Firstly, I am only able to use g_select to define the bottom bin for water droplet; could you please advise on indexing the bins from the bottom water layer? g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 1 -select 'resname SOL and res_com z 10' -on output-system.ndx How does one select SOL between z 10 and z 15, so on and so forth?Happy New Year, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to plot a droplet radius profile as a function of z-direction?
Dear gmx-users,Q1) I would like to plot the radius profile of a water droplet on graphene, as a function of z-direction, as per below:http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/largeWhich GROAMCS utility should I use, and how do I go about plotting the profile?Q2) Another question that I have is, suppose I have equilibrated (NVT) a water droplet for 10ns, and would like to plot the H-bond density (along the z-direction),I type the following command:g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 1 -sl 1000 -dens number -o number-density-OH.xvgI was only able to select:SystemGraphene (my substrate)WaterHow can I create a system.ndx such that it allows me to choose the OH (instead of water)?Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the time frame of 9 - 10 ns, but does it average the frames to give a time-averaged density.xvg?Thank you for your time, any feedback is appreciated.Merry Christmas Happy New Year!Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] BN parameters in MD
Dear all,I am wondering if anyone has computed the sp3-bonded BN using GROMACS?I am aware that GROMACS does not have boron in the force fields, and after much searching, I have only found some MD work on BN nanotubes.The question of whether GROMACS has the BN force field has also been asked a few times in this mail list it seems.The rest of the MD simulations on sp3-bonded BN are mostly employing the Tersoff potential.Does anyone know where I can get more information on the ffbonded parameters, specifically the Urey-Bradley potential (k-theta and kUB constants) [eq. 4.56 in manual], and the harmonic force constant (kb) [eq. 4.34]?Any info. is greatly appreciated.Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions
Dear Justin and Erik, Thank you for the feedback. I have also tried the following: i) separating OH- and Na+ ions ii) placing the ions much closer to water droplet iii) increase the spacing between each ions, i.e. using a larger box Perhaps I should try having the ions in a larger box, then fill the box with water molecules and then redo the energy minimisation and NVT? Well, like Erik said, there really isn't a smoking gun and what I'm observing might be either causative or symptomatic, there's just no way to know at this point. I don't know what good any of those three options will do, because I don't understand what you're trying to accomplish. What was the logic of putting a lattice of OH- and random Na+ in vacuo above a water droplet? What is the goal of your simulations?Thank you for the valuable input, the goal is to simulate the ions in water droplet.Instead of having a box of water with the charged ions, I used the water/graphene system that has been NVT equilibrated for 20ns, and placed the ions on top of the droplet.If adding 20 OH- and 20 Na+ proves to be problematic, is there a way to add the ions incrementally without attracting a large force?The OH- ions were arranged in such a way "genconf -nbox 4 5 1" as I have tried random insertion, using gmx insert-molecules, and have found that the ions were too close together.From my other previous calculations, adding a cluster of H3O+ and Cl- ions (ranging from 40 to 200 ions) on top of the water droplet worked fine with NVE and NVT.However, I have not been able to do so with OH- and Na+.Regards,Kester -Justin Regards, Kester On 11/10/14 5:04 AM, Erik Marklund wrote: Dear Kester, Hm. No obvious smoking gun as far as I can see. You could try a two-step minimisation where you first do one minimisation with soft-core potentials and then one without. What's strange to me is the lattice of OH- at the top of the box and the sodium ions that are floating out in the middle of nowhere. I don't understand the construction of this system, but having highly charged stuff in close contact and floating around in vacuum certainly looks like it could be trouble. -Justin Kind regards, Erik On 7 Nov 2014, at 05:36, Kester Wong wrote: Dear Erik, The starting structure consists of water on graphene that has already been energy minimised, and subsequently equilibrated (NVT) for 20ns. Using that (water droplet on graphene), I added the ions for energy minimisation. I followed a two-step minimisation: i) Minimisation with no constraints (-DFLEXIBLE) ii) Minimisation with constraints (SETTLES for TIPS3P water, and (-DCONSTRAINTS) for hydroxide) With the ions: I have tried placing the ions box lower toward water droplet, but the Max Force remains large upon energy minimisation. The input files can be accessed here: https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8usp=sharing The hydroxide parameter is taken from Gerrit Groenhof, based on the supplementary material in this paper: http://dx.doi.org/10.1016/j.bpj.2014.04.062 In short, this model was developed very similarly to the polarisable version of hydroxide in the SWM4-NDP force field. As for sodium and graphene, the topology parameters were taken from CHARMM27; TIPS3P was used for the water model. Visualisation after the energy minimisation showed a distorted virtual site of the hydroxide ions, where one of the four virtual sites no longer conform to the constraint. So, I am guessing whether the extremely large Max Force originates from the force constants in the hydroxide topology? Thank you for your time and assistance! -Kester - 원본 메일 - 보낸사람 : Erik Marklund 받는사람 : "" 받은날짜 : 2014년 11월 6일(목) 20:35:59 제목 : Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions Dear Kester, The potential energy is highly positive in the first case and the force is enormous in the second case, so no wonder that they blow up. How did you prepare these systems? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 6 Nov 2014, at 04:31, Kester Wong wrote: Dear all, I have been trying to energy minimise ~1980 water (tips3p) molecules with 20 OH- anions (with virtual sites and dummy atoms) and 20 Na+ cations, however, I always ended up getting a very large Max Force. Using emt
Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions
text/html; charset=UTF-8: Unrecognized -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Very large Max Force [Energy minimisation] in water with ions
Dear all,I have been trying to energy minimise ~1980 water (tips3p) molecules with 20 OH- anions (with virtual sites and dummy atoms) and 20 Na+ cations, however, I always ended up getting a very large Max Force.Using emtol = 1000 and emstep = 0.0001, I get:Potential Energy = 3.79607808453231e+09Maximum force = 9.86741557582003e+02 on atom 42394Norm of force = 2.38846729392462e+01Using emtol = 700 and emstep = 0.0001, I get:Potential Energy = -6.43566327273198e+13Maximum force = 9.24568347101016e+25 on atom 42262Norm of force = 5.74744822148669e+23As expected, both structures blew up during NVT equilibration.Could this be due to the arrangement of the ions? I tried separating the anions and cations in two boxes (placed on top of the water droplet), but that also yield a very large Max Force.FYI, the water droplet on graphene was equilibrated for 20ns.Any input is greatly appreciated. Thanks.- Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Assigning mass to a virtual site
Dear all,I am creating a topology file for hydroxide, closely following the parameters from the paper by Wolf et al:http://dx.doi.org/10.1016/j.bpj.2014.04.062This is somewhat similar to the polarisable hydroxide topology that was included in the recent SWM4-NDP force field.In this non-polarisable topology, I would like to know what atomic number should one label for the OH-OV2 type atom, as it was defined as a virtual site (but with 1 a.m.u assigned) in the paper's supporting material. I have labeled the atomic number with "X" as below:[ atomtypes ];name at.num mass charge ptype sigma epsilonOH-O 811.9980 -1.32 A0.00 0.00OH-H 11.00800 0.00 A0.14 0.2150576OH-OV1 00.0 0.00 D0.2916 0.2150576OH-OV2 X1.0 0.00 A0.25 0.2150576OH-qH 00.0 0.32 D0.00 0.00Can an atom (ptype=A) have zero at.num?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Assigning mass to a virtual site
Dear David and Justin,The SWM4-NDP force field was downloaded from virtualchemistry correct, but the non-polarisable version of the OH(with virtual sites) is not available, to the best of my knowledge. The section that describes the 1 a.m.u mass at the virtual site is available in the supporting material of the paper by Wolf et al. I will ask Wolf et al. and try to obtain the topology directly from the authour(s).Thanks for your assistance!Regards,Kester - 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 10월 29일(수) 22:14:12제목 : Re: [gmx-users] Assigning mass to a virtual site On 10/29/14 9:00 AM, David van der Spoel wrote: On 2014-10-29 13:19, Justin Lemkul wrote: On 10/29/14 6:32 AM, Kester Wong wrote: Dear all, I am creating a topology file for hydroxide, closely following the parameters from the paper by Wolf et al: http://dx.doi.org/10.1016/j.bpj.2014.04.062 This is somewhat similar to the polarisable hydroxide topology that was included in the recent SWM4-NDP force field. In this non-polarisable topology, I would like to know what atomic number should one label for the OH-OV2 type atom, as it was defined as a virtual site (but with 1 a.m.u assigned) in the paper's supporting material. I have labeled the atomic number with "X" as below: [ atomtypes ] ;name at.num masscharge ptype sigma epsilon OH-O8 11.9980 -1.32 A 0.000.00 OH-H1 1.00800 0.00 A 0.140.2150576 OH-OV1 0 0.0 0.00 D 0.2916 0.2150576 OH-OV2 X 1.0 0.00 A 0.250.2150576 OH-qH 0 0.0 0.32 D 0.000.00 Can an atom (ptype=A) have zero at.num? I would suggest you simply ask the authors to provide you with their topology. There are several details that are unclear to me, and I do not see anything that says the V1 or V2 sites carry any mass. Maybe I missed it due to a quick read-through, but this is in any case a very tricky setup. Don't reinvent the wheel; get the information straight from the people that did it. -Justin The topology is correct as downloaded from virtualchemistry.org. Good to know. I was afraid the OP was taking the hard way out and trying to do something from scratch that wasn't necessary :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to implement LJ 6-12 function form?
Dear all,I am using GROMACS 5.0, could anyone tell me how can I use the LJ 6-12 in my calculations?My force field [ defaults ] is as follows:[ defaults ]; nbfunccomb-rulegen-pairsfudgeLJ fudgeQQ12yes 0.5 0.5According to the manual, do I add "N" equals to 12 to enable the LJ 6-12 (carbon-water) interaction parameters to be used, without using the look up table "table6-12.xvg"?[ defaults ]; nbfunccomb-rulegen-pairsfudgeLJ fudgeQQ NLJ2yes 0.5 0.5 12My current system already has the following parameters bonding, nonbonding, graphene, water and ions topologies; based on the TIPS3P and CHARMM27 models.Thanks for any input!Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to implement LJ 6-12 function form?
I was puzzled by that before, as the LJ interactions by the Lorenzt-Berthelot comb-rules (page 68) looked exactly like the LJ 6-12 function form.Hence I was thinking how can one use the comb-rule type2 (carbon-water nonbond-param) and LJ 6-12 (table6-12.xvg) together.Thank you Eric!Cheers,Kester- 원본 메일 -보낸사람 : Eric Smoll ericsm...@gmail.com받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 10월 29일(수) 10:51:54제목 : Re: [gmx-users] How to implement LJ 6-12 function form?Hello Kester, Setting the first value in the defaults directive to 1 indicates that you want to use the 6-12 LJ potential. As far as I understand, setting N is only necessary if you want the repulsive LJ term to be something other than 12. I don't think you need to do anything else. The first defaults entry looks good. See page 144 of the Gromacs 5.0.2 manual. Best, Eric On Tue, Oct 28, 2014 at 7:40 PM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear all, I am using GROMACS 5.0, could anyone tell me how can I use the LJ 6-12 in my calculations? My force field [ defaults ] is as follows: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 According to the manual, do I add "N" equals to 12 to enable the LJ 6-12 (carbon-water) interaction parameters to be used, without using the look up table "table6-12.xvg"? [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQN LJ 2 yes 0.5 0.5 12 My current system already has the following parameters bonding, nonbonding, graphene, water and ions topologies; based on the TIPS3P and CHARMM27 models. Thanks for any input! Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] charge group moved too far between two domain decomposition step
.24 #endif I would appreciate it if anyone could point me to the right direction, once and for all. For constraints in a system with tips3p.itp, and hydronium.itp, how does one define "FLEXIBLE" or "CONSTRAINTS"? define = -DFLEXIBLE in the .mdp file. See the manual. I ought to write the question differently, I was meant to ask, how does one tell GROMACS not to impose constraints on both water and hydronium. Below is the .itp for the hydronium model: [ moleculetype ] ; molname nrexcl H3O 2 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 H3O-O1 H3O OW 1 -0.59 15.9994 2 H3O-H1 H3O H31 1 0.53 1.008 3 H3O-H1 H3O H32 1 0.53 1.008 4 H3O-H1 H3O H33 1 0.53 1.008 ; use #ifdef FLEXIBLE or #ifdef CONSTRAINTS #ifdef FLEXIBLE [ bonds ] ;i j funct length (nm) force.c. (kJ/mol) 1 2 1 0.102 ; Hydronium OH bond 1 3 1 0.102 ; Wolf used 1000? check this 1 4 1 0.102 ; Hub used 400,000 [ angles ] ; i j k funct angle force.c. 21 3 1 112 ; Hub used 400 force 41 3 1 112 21 4 1 112 #else [ constraints ] ; ifunct dohdhh 1 2 2 0.102 1 3 2 0.102 1 4 2 0.102 2 3 2 0.169124 3 4 2 0.169124 2 4 2 0.169124 #endif [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 I tried the two approaches, by either having define = -DFLEXIBLE in my .mdp file, or #define FLEXIBLE in my topol.top file, Either using the "define" keyword or explicitly using #define in the topology will trigger the same behavior. The more flexible approach is to use .mdp settings, lest you perhaps forget one day and end up doing the run incorrectly because you forgot you hacked the topology! Thanks for the tip! Yes, I do make changes more regularly on .mdp, less so on the topology; one can forget to amend the topology for that matter.Thank you for your input Justin!Regards,Kester-Justin and received this error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond. Setting the LD random seed to 3234307754 Generated 207 of the 210 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 210 of the 210 1-4 parameter combinations Thank you for your time and patience. Regards, Kester Mark Cheers, Kester You should start by using a time step more appropriate to your use of constraints = none, or vice versa. Mark On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong wrote: Dear all, I am intrigued by the error that I have received this morning, as follows: The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Y distance out of cell 7.144197 Old coordinates: 54.499 39.697 14.058 New coordinates: 54.499 39.697 14.058 Old cell boundaries in direction Y: 19.468 32.846 New cell boundaries in direction Y: 18.667 32.553 If the charge group moved, if any, then shouldn't the new coordinates be showing different values? It was a new NPT calculation that I continued from a 20ns NVT run, so it should be equilibrated well enough, for a simple water on graphene system. Using GROMACS 5.0, I was unable to start the NPT with Berendsen thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my tau-T was 0.5, following the general rule of thumb, that tau-P should be larger than tau-T to allow thermal degrees of freedom to equilibrate faster than the box size). Should I reduce tau-P? Below is my NPT.mdp parameters: ; RUN CONTROL PARAMETERS integrator = md tinit= 2.000 dt = 0.002; 2 fs nsteps = 500 ; 10,000 ps comm-mode= Linear nstcomm = 10 emtol= 0.001 niter= 30 ; OUTPUT CONTROL OPTIONS nstxout = 5000; save coordinates every 8 ps nstvout
Re: [gmx-users] charge group moved too far between two domain decomposition step
Thanks for the input Mark,<kester2...@ibs.re.kr> Hi Mark, Thanks for the input, I thought a time step of 2 fs is small enough? Not always for unconstrained bonds. The largest stable time step is determined by the size of the period of the fastest oscillation, which is vibrations of bonds to hydrogen. 2fs stretches the friendship there, and you would certainly want to equilibrate thoroughly at a smaller time step if you are doing messy things like freezing nanotubes and using pressure coupling (which would not be my go-to method without a clear demonstration that it produces valid results). More generally, equilibration of a not-quite-right structure works better with a smaller timestep, because that copes better with the artificially large forces you get... Thanks for the very informative input, this should serve me well as a rule of thumb for other systems as well.<kester2...@ibs.re.kr> Should I change my constraint to constraints = h-bonds instead? That would be normal. Or, Should I use: dt = 0.001; 1 fs constraints = none constraint-algorithm = shake Plausible, but you want to run the final simulation with constraints for the higher ns/day you obtain... I think I got a little confused here.For energy minimisation, I should impose no constraints to obtain the most realistic starting structure for NVT.As for NVT, one should use constraints to achieve a much quicker equilibration, is that correct?For instance (TIPS3P.itp as shown below), to achieve a higher ns/day in my NVT run, I should have constraints = none in my mdp setting (using [bonds] and [angles]);or have define = -DFLEXIBLE in my .mdp setting to achieve a better energy minimisation (using SETTLES)?[ moleculetype ]; molname nrexclSOL 2[ atoms ]; id at type res nr residu name at name cg nr charge1OT 1SOL OW 1-0.8342HT 1SOL HW1 10.4173HT 1SOL HW2 10.417#ifndef FLEXIBLE[ settles ]; ij funct length1 1 0.09572 0.15139[ exclusions ]1 2 32 1 33 1 2#else[ bonds ]; i jfunct length force.c.1210.09572 376560.0 0.09572376560.01310.09572 376560.0 0.09572376560.0[ angles ]; i j kfunct angle force.c.21 31104.52 460.24 104.52 460.24#endif<kester2...@ibs.re.kr><kester2...@ibs.re.kr>I would appreciate it if anyone could point me to the right direction, once and for all. For constraints in a system with tips3p.itp, and hydronium.itp, how does one define "FLEXIBLE" or "CONSTRAINTS"?Below is the .itp for the hydronium model:[ moleculetype ] ; molname nrexcl H3O 2 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 H3O-O1 H3O OW 1 -0.59 15.9994 2 H3O-H1 H3O H31 1 0.53 1.008 3 H3O-H1 H3O H32 1 0.53 1.008 4 H3O-H1 H3O H33 1 0.53 1.008 ; use #ifdef FLEXIBLE or #ifdef CONSTRAINTS #ifdef FLEXIBLE [ bonds ] ;i j funct length (nm) force.c. (kJ/mol) 1 2 1 0.102 ; Hydronium OH bond 1 3 1 0.102 ; Wolf used 1000? check this 1 4 1 0.102 ; Hub used 400,000 [ angles ] ; i j k funct angle force.c. 21 3 1 112 ; Hub used 400 force 41 3 1 112 21 4 1 112 #else [ constraints ] ; ifunct dohdhh 1 2 2 0.102 1 3 2 0.102 1 4 2 0.102 2 3 2 0.169124 3 4 2 0.169124 2 4 2 0.169124 #endif [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 I tried the two approaches, by either having define = -DFLEXIBLE in my .mdp file, or #define FLEXIBLE in my topol.top file,and received this error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond.Setting the LD random seed to 3234307754 Generated 207 of the 210 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 210 of the 210 1-4 parameter combinations Thank you for your time and patience.Regards,Kester<kester2...@ibs.re.kr> Mark Cheers, Kester You should start by using a time step more appropriate to your use of constraints = none, or vice versa. Mark On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong wrote: Dear all, I am intrigued by the error that I have received this morning, as follows: The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Y distance out of cell 7.144197 Old coordinates: 54.499 39.697 14.058 New coordinates: 54.499 39.697 14.058 Old cell boundaries in direct
[gmx-users] charge group moved too far between two domain decomposition steps?
Dear all,I am intrigued by the error that I have received this morning, as follows:The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Ydistance out of cell 7.144197Old coordinates: 54.499 39.697 14.058New coordinates: 54.499 39.697 14.058Old cell boundaries in direction Y: 19.468 32.846New cell boundaries in direction Y: 18.667 32.553If the charge group moved, if any, then shouldn't the new coordinates be showing different values?It was a new NPT calculation that I continued from a 20ns NVT run, so it should be equilibrated well enough, for a simple water on graphene system.Using GROMACS 5.0, I was unable to start the NPT with Berendsen thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my tau-T was 0.5, following the general rule of thumb, that tau-P should be larger than tau-T to allow thermal degrees of freedom to equilibrate faster than the box size).Should I reduce tau-P?Below is my NPT.mdp parameters:; RUN CONTROL PARAMETERSintegrator= mdtinit = 2.000dt= 0.002 ; 2 fsnsteps = 500 ; 10,000 pscomm-mode= Linearnstcomm = 10emtol = 0.001niter = 30; OUTPUT CONTROL OPTIONSnstxout = 5000 ; save coordinates every 8 psnstvout = 5000 ; save velocities every 8 psnstfout = 0nstlog = 5000 ; update log file every 8 psnstenergy= 5000 ; save energies every 8 ps;nstxtcout is replaced with nstxout-compressednstxout-compressed= 5000 ; no. of steps between writing coordinates using lossy compression;xtc-precision is replaced with compressed-x-precisioncompressed-x-precision = 3000 ; precision with which to write to the compressed trajectory file; Periodic boundary conditions: xyz (default), no (vacuum)cutoff-scheme = Verlet ; default for GROMACS-5.0nstlist = 1 ; A smaller nstlist may reduce LINCS warningsns-type = grid ;pbc = xyz;periodic_molecules= yes ; cannot be used with SHAKE; nblist cut-offrlist = 1.40 ; short-range neighbourlist cutoffnstcalclr= 1coulombtype = PMEcoulomb-modifier = Potential-shift-Verletr_coulomb= 1.40 ; short-range electrostatic cutoffrcoulomb-switch = 0 ; used when potential-switch (coulomb-modifier) is specifiedepsilon-r= 1 ; default value=1pme_order= 4fourierspacing = 0.12fourier_nx= 0fourier_ny= 0fourier_nz= 0ewald_rtol= 1e-05ewald_geometry = 3depsilon_surface = 0 ; Use 0 when simulation is done with PME;vdw-type = switch is replaced with the following two flags in GROMACS-5.0vdwtype = Cut-offvdw_modifier = Potential-switch; cut-off lengthsrvdw-switch = 1.00rvdw = 1.40 ; short-range van der Waals cutoffconstraints = noneconstraint-algorithm = SHAKEcontinuation = yes ; starting from NVT runShake-SOR= noshake-tol= 0.0001;lincs-order = 4 ; accuracy of LINCS;lincs-iter= 24 ; also related to accuracy; Lincs will write a warning to the stderr if in one step a bond; rotates over more degrees than;lincs-warnangle = 30Tcoupl = v-rescalenh-chain-length = 1 ; the leapfrog md integrator only supports 1; Groups to couple separatelytc-grps = GRA SOL; Time constant (ps) and reference temperature (K)tau-t = 0.5 0.5ref-t = 300 300nsttcouple= 20 ; added by k-wong ; not specified in Yanbin's MDPPcoupl = Parrinello-RahmanPcoupltype= isotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau-p = 5.0 ; time constant in pscompressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1ref-p = 1.0 ; reference pressure, in bar; Non-equilibrium MD stufffreezegrps= GRAfreezedim= Y Y Ygen_vel = no;gen_temp = 300;gen_seed = 173529Thanks in advance!Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] charge group moved too far between two domain decomposition step
Hi Mark,Thanks for the input, I thought a time step of 2 fs is small enough?Should I change my constraint to constraints = h-bonds instead?Or,Should I use:dt = 0.001; 1 fsconstraints = noneconstraint-algorithm = shakeCheers,Kester You should start by using a time step more appropriate to your use of constraints = none, or vice versa. Mark On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear all, I am intrigued by the error that I have received this morning, as follows: The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Y distance out of cell 7.144197 Old coordinates: 54.499 39.697 14.058 New coordinates: 54.499 39.697 14.058 Old cell boundaries in direction Y: 19.468 32.846 New cell boundaries in direction Y: 18.667 32.553 If the charge group moved, if any, then shouldn't the new coordinates be showing different values? It was a new NPT calculation that I continued from a 20ns NVT run, so it should be equilibrated well enough, for a simple water on graphene system. Using GROMACS 5.0, I was unable to start the NPT with Berendsen thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my tau-T was 0.5, following the general rule of thumb, that tau-P should be larger than tau-T to allow thermal degrees of freedom to equilibrate faster than the box size). Should I reduce tau-P? Below is my NPT.mdp parameters: ; RUN CONTROL PARAMETERS integrator = md tinit= 2.000 dt = 0.002; 2 fs nsteps = 500 ; 10,000 ps comm-mode= Linear nstcomm = 10 emtol= 0.001 niter= 30 ; OUTPUT CONTROL OPTIONS nstxout = 5000; save coordinates every 8 ps nstvout = 5000; save velocities every 8 ps nstfout = 0 nstlog = 5000; update log file every 8 ps nstenergy= 5000; save energies every 8 ps ;nstxtcout is replaced with nstxout-compressed nstxout-compressed = 5000; no. of steps between writing coordinates using lossy compression ;xtc-precision is replaced with compressed-x-precision compressed-x-precision = 3000; precision with which to write to the compressed trajectory file ; Periodic boundary conditions: xyz (default), no (vacuum) cutoff-scheme= Verlet ; default for GROMACS-5.0 nstlist = 1 ; A smaller nstlist may reduce LINCS warnings ns-type = grid ; pbc = xyz ;periodic_molecules = yes ; cannot be used with SHAKE ; nblist cut-off rlist= 1.40 ; short-range neighbourlist cutoff nstcalclr= 1 coulombtype = PME coulomb-modifier = Potential-shift-Verlet r_coulomb= 1.40 ; short-range electrostatic cutoff rcoulomb-switch = 0 ; used when potential-switch (coulomb-modifier) is specified epsilon-r= 1 ; default value=1 pme_order= 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 ; Use 0 when simulation is done with PME ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0 vdwtype = Cut-off vdw_modifier = Potential-switch ; cut-off lengths rvdw-switch = 1.00 rvdw = 1.40 ; short-range van der Waals cutoff constraints = none constraint-algorithm = SHAKE continuation = yes; starting from NVT run Shake-SOR= no shake-tol= 0.0001 ;lincs-order = 4 ; accuracy of LINCS ;lincs-iter = 24; also related to accuracy ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than ;lincs-warnangle = 30 Tcoupl = v-rescale nh-chain-length = 1; the leapfrog md integrator only supports 1 ; Groups to couple separately tc-grps = GRA SOL ; Time constant (ps) and reference temperature (K) tau-t= 0.5 0.5 ref-t= 300 300 nsttcouple = 20 ; added by k-wong ; not specified in Yanbin's MDP Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and refer
Re: [gmx-users] SWM4-NDP force field
Hi Dr. Chaban,The four dummy atoms carry a mass of 1 a.m.u each, hence the oxygen mass of 11.998.However, what I don't understand is that the same atom has a mass of 0.0 under [ atomtypes ].For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-) ions, if there is nonbonding-parameters specified, will having a different fudge value (0.5 instead of 1.0) make a difference?Thank you in advance.Regards,Kester- 원본 메일 -보낸사람 : "Dr. Vitaly Chaban" vvcha...@gmail.com받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 10월 18일(토) 16:20:49제목 : Re: [gmx-users] SWM4-NDP force fieldThe assigned masses are due to the presence of dummy atoms. The model molecule must represent moments of inertia. 1-4 (fudgeLJ and fudgeQQ) interactions do not apply for water. So, you care about a larger molecule only. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 18, 2014 at 8:39 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear all, I would like to know if this would cause a difference in MD calculations (text highlighted in red): The assigned mass for the hydroxide O-atom seems to be inconsistent. Was the zero atomic mass set with a specific purpose? #define SHELLPTYPE S #define SHELLMASS 0 #define OXYGENMASS 15.9994 [ atomtypes ] ; name btype masscharge ptype sigmaepsilon SWM4-NDP_110a ODSHELLMASS-1.71636SHELLPTYPE 0.0 0.0 SWM4-NDP_OV1 OV1 1.00.0 A 0.24 0.294191 SWM4-NDP_OV2 OV2 0.00.0 D 0.28 0.294191 SWM4-NDP_H H 1.008 0.0 A 0.07 0.294191 SWM4-NDP_qHqH 0.0 0.23 D 0.0 0.0 SWM4-NDP_O O 0.0 0.203 A 0.0 0.0 ; Hydroxide [ moleculetype ] ; molname nrexcl OH-2 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1SWM4-NDP_O 1 OH- O 1 0.202 11.998 2SWM4-NDP_110a1 OH- OS 1 -1.432 0.00 3SWM4-NDP_H 1 OH- H 1 0.001.008 4SWM4-NDP_OV1 1 OH- OV1 1 0.001.0 5SWM4-NDP_OV1 1 OH- OV1 1 0.001.0 6SWM4-NDP_OV1 1 OH- OV1 1 0.001.0 7SWM4-NDP_OV1 1 OH- OV1 1 0.001.0 8SWM4-NDP_OV2 1 OH- OV2 1 0.000.00 9SWM4-NDP_qH 1 OH- qH 1 0.230.00 [ polarization ] #ifdef POL2WATER 1 2 2 0.00068090.02 16.736e8 #else 1 2 1 0.0006809 #endif ; Initialy developed as a harmonic bond ; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) = 138.9354492 * sqrt(qS)/k ; [ bonds ] ; 1 2 6 0.0 418400 [ constraints ] 3 1 1 0.0968 4 1 1 0.1463 5 1 1 0.1463 6 1 1 0.1463 7 1 1 0.1463 4 6 1 0.1979 6 5 1 0.1979 5 7 1 0.1979 7 4 1 0.1979 #ifdef CONSTRAINTS [ constraints ] 3 4 1 0.15 3 5 1 0.15 3 6 1 0.15 ; A fourth constraint would make the system redundant and therefore ; numerically unstable. ; 3 7 1 0.15 #else [ angles ] 3 1 4 1 73.11 683 3 1 5 1 73.11 683 3 1 6 1 73.11 683 3 1 7 1 73.11 683 #endif [ dummies2 ] 8 3 1 11.4390 9 3 1 1 -0.3099 [ exclusions ] 1 2 3 4 5 6 7 8 9 2 1 3 4 5 6 7 8 9 3 1 2 4 5 6 7 8 9 4 1 2 3 5 6 7 8 9 5 1 2 3 4 6 7 8 9 6 1 2 3 4 5 7 8 9 7 1 2 3 4 5 6 8 9 8 1 2 3 4 5 6 7 9 9 1 2 3 4 5 6 7 8 If I am to add/define graphene's bonded and nonbonded parameters into the SWM4-NDP force field, using CHARMM27 parameters, should I take into consideration the fudgeLJ and fudgeQQ differences (0.5 fudge LJ and fudgeQQ in SWM4-NDP, 1.0 for fudgeLJ and fudgeQQ in CHARMM27)? The comb-rules are the same (no.2). Thanks in advance! Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or sen
[gmx-users] SWM4-NDP force field
Dear all,I would like to know if this would cause a difference in MD calculations (text highlighted in red):The assigned mass for the hydroxide O-atom seems to be inconsistent. Was the zero atomic mass set with a specific purpose?#define SHELLPTYPE S#define SHELLMASS 0#define OXYGENMASS 15.9994[ atomtypes ]; name btype mass charge ptype sigmaepsilonSWM4-NDP_110a OD SHELLMASS -1.71636 SHELLPTYPE 0.0 0.0SWM4-NDP_OV1 OV1 1.0 0.0 A0.24 0.294191SWM4-NDP_OV2 OV2 0.0 0.0 D0.28 0.294191SWM4-NDP_H H1.008 0.0 A0.07 0.294191SWM4-NDP_qH qH 0.0 0.23 D0.0 0.0SWM4-NDP_O O0.0 0.203 A0.0 0.0; Hydroxide[ moleculetype ]; molnamenrexclOH- 2[ atoms ]; id at type res nr residu name at name cg nr charge mass1 SWM4-NDP_O1OH-O 10.202 11.9982 SWM4-NDP_110a 1OH- OS 1 -1.432 0.003 SWM4-NDP_H1OH-H 10.00 1.0084 SWM4-NDP_OV1 1OH- OV1 10.00 1.05 SWM4-NDP_OV1 1OH- OV1 10.00 1.06 SWM4-NDP_OV1 1OH- OV1 10.00 1.07 SWM4-NDP_OV1 1OH- OV1 10.00 1.08 SWM4-NDP_OV2 1OH- OV2 10.00 0.009 SWM4-NDP_qH 1OH- qH 10.23 0.00[ polarization ]#ifdef POL2WATER1 2 2 0.00068090.02 16.736e8#else1 2 1 0.0006809#endif; Initialy developed as a harmonic bond; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) = 138.9354492 * sqrt(qS)/k; [ bonds ]; 1 2 6 0.0 418400[ constraints ]3 1 1 0.09684 1 1 0.14635 1 1 0.14636 1 1 0.14637 1 1 0.14634 6 1 0.19796 5 1 0.19795 7 1 0.19797 4 1 0.1979#ifdef CONSTRAINTS[ constraints ]3 4 1 0.153 5 1 0.153 6 1 0.15; A fourth constraint would make the system redundant and therefore; numerically unstable.; 3 7 1 0.15#else[ angles ]3 1 4 1 73.11 6833 1 5 1 73.11 6833 1 6 1 73.11 6833 1 7 1 73.11 683#endif[ dummies2 ] 8 3 1 1 1.4390 9 3 1 1 -0.3099[ exclusions ]1 2 3 4 5 6 7 8 92 1 3 4 5 6 7 8 93 1 2 4 5 6 7 8 94 1 2 3 5 6 7 8 95 1 2 3 4 6 7 8 96 1 2 3 4 5 7 8 97 1 2 3 4 5 6 8 98 1 2 3 4 5 6 7 99 1 2 3 4 5 6 7 8If I am to add/define graphene's bonded and nonbonded parameters into the SWM4-NDP force field, using CHARMM27 parameters, should I take into consideration the fudgeLJ and fudgeQQ differences (0.5 fudge LJ and fudgeQQ in SWM4-NDP, 1.0 for fudgeLJ and fudgeQQ in CHARMM27)? The comb-rules are the same (no.2).Thanks in advance!Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with constraints in NVT calculations.
Hi Justin and all, Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the graphene-water interface Of course you can implement whatever you like. Gromacs has been able to carry out polarizable simulations for a very long time; I've only ever cautioned against abuse of certain models. I guess that GROMACS is capable in running polarisable sims, but for the Drude polarisable calcs, they are prone to polarisation catastrophe due to the massless shells and thermostat instability? Polarization catastrophe is possible in any polarizable simulation. Usually very small time steps are required to avoid this, unless using an anharmonic potential or a hard wall restraint. Using Morse = yes for the anharmonic potential option, whereas using the parameters below for the hard wall restraint option? pbc = xy nwall = 2 wall-atomtype =; optional wall-type = 12-6 wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run wall-density = 5 5 wall-ewald-zfac = 3 No. I'm not suggesting a Morse potential. What I was referring to was an anharmonic function for the bonds, which is present in Gromacs but I'm not sure if it's documented. The wall settings in Gromacs have nothing to do with this. Such a function is not present in Gromacs (yet). Although the wall settings have nothing to do with polarisation catastrophe, I guess it might be useful in the following case:I have been using a time step of 1 fs, which is small already, yet the water droplet (on graphene) quickly fills up the vacuum of ~5-6 nm along the z-direction. I will try using the wall setup as above, hoping that water remains a droplet with the presence of H3O and Cl ions. Could you please explain what is the difference between the three types of wall; 9-3, 10-4, and 12-6?The only part of the GROMACS 5.0 manual that described anharmonic bond potential is in the Morse potential section 4.2.2.Which function is not available in GROMACS yet? In the paper mentioned above, the authors have carried out three types of cals: i) SPC/E on non-pol graphene ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite charge): graphene-DP in neutral or charged states They seemed to have simulated their systems using both additive and polarisable (0.878 angstrom^3) models? I guess this is where I got confused. I suppose you can make any model work if you parametrize it a certain way, but my point in the previous message is that you shouldn't go off trying to build a force field that has SWM4-NDP water around additive CHARMM solutes. Yep, now I understand it. If I wanted to also describe graphene, is it possible to include carbon parameters in the SWM4-NDP force field then? Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force field, you're creating a force field that describes both. This can certainly be done if you have all the parameters. That is great! To create a FF that describes the SWM4 water, NDP ions, and graphene carbon (CA); I will have to include graphene.itp, the CA-CA bonded parameters, and the LJ nonbonding interaction parameters, is that right? On the side: From my previous calcs using GRAPPA force field (TIPS3P water model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water into thin layer. But that was polarisable graphene in a rigid rod model (dummy instead of shelltype particle). Pardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom? In the Drude model with 0.4-amu particles, the Drudes are essentially just atoms. There's nothing conceptually special about them, we just handle them slightly differently in the code. Well since domain decomposition will not work on shelltype calcs, I am intrigued to experiment if I can: i) replace the Drudes to atom with the same configuration - opposite charge, mass (0.4 amu), lengths, etc The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have their positions integrated (extended Lagrangian) separately from "normal" atoms. Conceptually, a 0.4-amu Drude is just
Re: [gmx-users] v-rescale fatal error
Hi Mark,The H3O ion topology is defined as follows:; Hydronium and hydroxide parameters developend by M.G. Wolf; Hydronium[ moleculetype ]; molnamenrexclH3O 2[ atoms ]; id at type res nr residu name at name cg nr charge mass1SWM4-NDP_O2 1H3O O2 10.8522SWM4-NDP_110b 1H3O OA 1 -1.124 ; modified3SWM4-NDP_H2 1H3O H31 10.4244SWM4-NDP_H2 1H3O H32 10.4245SWM4-NDP_H2 1H3O H33 10.424[ polarization ]#ifdef POL2WATER1 2 2 0.00041950.02 16.736e8#else1 2 1 0.0004195#endif; Initialy developed as a harmonic bond; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) = 138.9354492 * sqrt(qS)/k; [ bonds ]; 1 2 6 0 418400#ifdef FLEXIBLE[ bonds ]1310.102 401410.102 401510.102 40[ angles ]31 41109.47 40031 51109.47 40041 51109.47 400#else[ constraints ]; i funct doh dhh1 3 10.1021 4 10.1021 5 10.1023 4 10.1691244 5 10.1691243 5 10.169124#endif[ exclusions ]1234521345312454123551234For example, within the SWM4-NDP system containing 2 ions that I have defined, I get something like this:Number of degrees of freedom in T-Coupling group GRA is 0.00Number of degrees of freedom in T-Coupling group SOL is 11985.00Number of degrees of freedom in T-Coupling group H3O is 9.00Number of degrees of freedom in T-Coupling group Cl- is 3.00I was able to then obtain the .tpr file, however, once the job is submitted, the fatal error reads:Inner product between old and new vector = 0.0!constraint #5 atoms 46282 and 46283Wrote pdb files with previous and current coordinatesInner product between old and new vector = 0.0!constraint #4 atoms 46281 and 46283Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#Wrote pdb files with previous and current coordinatesstarting mdrun 'Water with ions'500 steps, 5000.0 ps.Inner product between old and new vector = 0.0!constraint #5 atoms 46282 and 46283Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#Wrote pdb files with previous and current coordinates---Program gmx_mpi, VERSION 5.0Source code file: /share/gromacs-5.0/src/gromacs/mdlib/coupling.c, line: 1439Fatal error:The v-rescale thermostat was called with a group with #DOF=2.999250, but for #DOF3 only integer #DOF are supportedFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors---The SWM4-NDP file can be downloaded directly from virtualchemistry.orgCheers,Kester- 원본 메일 -보낸사람 : Mark Abraham mark.j.abra...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2014년 10월 10일(금) 21:35:03제목 : Re: [gmx-users] v-rescale fatal errorHi Kester, Glad it's resolved. I am curious what (H3O+?) molecule definition led to that computation of the DOF? That code is not tested at all... Mark On Fri, Oct 10, 2014 at 2:03 PM, Kester Wong <kester2...@ibs.re.kr> wrote: Hi Justin and all, The same mistake will not be repeated. The ions are now defined in the residuetypes.dat file and should be grouped together. -From lessons learned, comes better performance. Thank you all. Kester - 원본 메일 - *보낸사람* : Justin Lemkul <jalem...@vt.edu> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 10월 10일(금) 20:38:56 *제목* : Re: [gmx-users] v-rescale fatal error On 10/10/14 7:36 AM, Kester Wong wrote: Hi Mark, I think it was due to the charged groups in my temp. coupling setting; I had the H3O cation(s) and Cl anion(s) grouped separately: tc-grps = GRA SOL H3O Cl- ; Time constant (ps) and reference temperature (K) tau-t= 0.5 0.5 0.5 0.5 ref-t= 300 300 300 300 Calculations run fine once I grouped the ions together, or water+ions. You shouldn't couple ions separately from the solvent; that's just not stable. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting
Re: [gmx-users] v-rescale fatal error
Hi Justin and all,The same mistake will not be repeated.The ions are now defined in the residuetypes.dat file and should be grouped together.-From lessons learned, comes better performance.Thank you all.Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 10월 10일(금) 20:38:56제목 : Re: [gmx-users] v-rescale fatal errorOn 10/10/14 7:36 AM, Kester Wong wrote: Hi Mark, I think it was due to the charged groups in my temp. coupling setting; I had the H3O cation(s) and Cl anion(s) grouped separately: tc-grps = GRA SOL H3O Cl- ; Time constant (ps) and reference temperature (K) tau-t= 0.5 0.5 0.5 0.5 ref-t= 300 300 300 300 Calculations run fine once I grouped the ions together, or water+ions. You shouldn't couple ions separately from the solvent; that's just not stable. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] v-rescale fatal error
Dear all,I wanted to use v-rescale thermostat for a NVT run, however, I have been getting error as such:The v-rescale thermostat was called with a group with #DOF=2.999250, but for #DOF3 only integer #DOF are supportedHas anyone experienced similar issue before? I could not find much information about it online.Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with constraints in NVT calculations.
Hi Justin, Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the graphene-water interface Of course you can implement whatever you like. Gromacs has been able to carry out polarizable simulations for a very long time; I've only ever cautioned against abuse of certain models. I guess that GROMACS is capable in running polarisable sims, but for the Drude polarisable calcs, they are prone to polarisation catastrophe due to the massless shells and thermostat instability?In the paper mentioned above, the authors have carried out three types of cals:i) SPC/E on non-pol graphene ii) SWM4-DP on non-pol graphene: graphene in neutral or charged statesiii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite charge): graphene-DP in neutral or charged statesThey seemed to have simulated their systems using both additive and polarisable (0.878 angstrom^3) models?I guess this is where I got confused.On the side: From my previous calcs using GRAPPA force field (TIPS3P water model), graphene's polarisation (0.91angstrom^3) resulted in spreading of water into thin layer. But that was polarisable graphene in a rigid rod model (dummy instead of shelltype particle). Pardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom? In the Drude model with 0.4-amu particles, the Drudes are essentially just atoms. There's nothing conceptually special about them, we just handle them slightly differently in the code. Well since domain decomposition will not work on shelltype calcs, I am intrigued to experiment if I can:i) replace the Drudes to atom with the same configuration - opposite charge, mass (0.4 amu), lengths, etcORii) switch to the more stable SWM4-DP with the hydronium and hydroxide implementation from David van der Spoel?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with constraints in NVT calculations.
Hi Justin,Thank you for the clarification. I should look into using NAMD.The new polarisable Drude implementation will surely benefit everyone in the MD community.I am looking forward to using it, as with others (I think there was a similar post by Yana Tsoneva on this issue too, dated back in July).Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolotitled: Polarizability effects in molecular dynamics simulations of the graphene-water interfacePardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model?The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 10월 8일(수) 03:02:12제목 : Re: [gmx-users] Problem with constraints in NVT calculations. On 10/6/14 10:35 PM, Kester Wong wrote: Dear Justin and all, 원본 메일 - *보낸사람* : Justin Lemkul <jalem...@vt.edu> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 9월 29일(월) 21:32:13 *제목* : Re: [gmx-users] Problem with constraints in NVT calculations. On 9/29/14 8:01 AM, Kester Wong wrote: Dear all, I have been using the SWM4-NDP water model that works well with CHARMM27 force field. Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive force field. The two are not compatible. If you're using them together, you're basically just gambling that they work. You shouldn't do this. Thank you for the information. Actually, I took the data from the ff-drude-water-ions.itp file and included them in the CHARMM27 itp files. Now I realised that it does not work like that. If the ffnonbonded.itp file contains the appropriate nonbonded parameters for the polarisable water model (i.e. the atomtypes and dummies for the Drude water and ions model), will it work? Below is my input topologies: https://drive.google.com/file/d/0B7ym8d6G9-e2dmdQOHNaU3c3Qkk/view?usp=sharing No, this is fundamentally wrong. You can't simply combine some additive components and some polarizable components and hope for a sensible physical model. Force fields are derived in self-consistent ways. You can't patch them together. The force field (most recent version) was obtained from virtualchemistry, and consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. The water on graphene (energy minimisation and NVT) calculations are stable, and have produced a few NVT runs of up to 10ns. I also compared the NVT runs with other previously calculated structures, namely, the visualised NVT runs are very much comparable to that obtained by CHARMM27 force field with TIPS3P water model. However, as the polarisable H3O+ and Cl- ions are inserted into the simulation box, the NVT run tends to crash as a result of too many LINCS warnings. I suspect that the constraints in the H3O is the cause of the LINCS warnings, and after removing the [ constraints ] in the topology file, the calculation seems to be running. ;[ constraints ] ;; i funct doh dhh ;1 3 1 0.102 ;1 4 1 0.102 ;1 5 1 0.102 ;3 4 1 0.169124 ;4 5 1 0.169124 ;3 5 1 0.169124 Can anyone please tell me if what I am doing is correct? As I am not sure if removing the H3O constraints in the NVT run is appropriate. With regard to the massless Drude and standard oxygen mass (thank you Justin for providing the information), I would like to know why are they not appropriate (as mentioned in the previous email) for the SWM4-NDP model? I wasn't making a declarative statement that it won't work. I was asking whether anyone had verified that using a massless Drude in that model actually reproduced all of the physical properties of the SWM4-NDP model. We do all of our development on the Drude FF with Drudes of mass = 0.4 amu and the extended Lagrangian. I don't know how a massless Drude behaves in this model. It may work fine, but you should very rigorously verify this yourself before doing anything by doing simulations of pure water. -Justin I have Read the paper by Jochen Hub et al [Chem. Sci., 5, 1745 2013], that their calculated data (water with ions) are in line with experimental results. Upon further inspection, I found more papers that reported the us
[gmx-users] Polarisable (hydronium and hydroxide) model compatible with graphene?
Dear All,Until now, I have tried using TIPS3P and SWM4-NDP water models, to which I am unsuccessful in modelling water+ions on graphene.The nature of my research topic requires a charged model, which means using polarisable force field is most probably the best option.Could anyone recommend a reliable force field that I could use to simulate polarisable water+ions on graphene?I really really am grateful for any help I can get.- Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with constraints in NVT calculations.
Dear all,I have been using the SWM4-NDP water model that works well with CHARMM27 force field.The force field (most recent version) was obtained from virtualchemistry, and consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al.The water on graphene (energy minimisation and NVT) calculations are stable, and have produced a few NVT runs of up to 10ns.I also compared the NVT runs with other previously calculated structures, namely, the visualised NVT runs are very much comparable to that obtained by CHARMM27 force field with TIPS3P water model.However, as the polarisable H3O+ and Cl- ions are inserted into the simulation box, the NVT run tends to crash as a result of too many LINCS warnings.I suspect that the constraints in the H3O is the cause of the LINCS warnings, and after removing the [ constraints ] in the topology file, the calculation seems to be running.;[ constraints ];; i funct doh dhh;1 3 10.102;1 4 10.102;1 5 10.102;3 4 10.169124;4 5 10.169124;3 5 10.169124Can anyone please tell me if what I am doing is correct?As I am not sure if removing the H3O constraints in the NVT run is appropriate.With regard to the massless Drude and standard oxygen mass (thank you Justin for providing the information), I would like to know why are they not appropriate (as mentioned in the previous email) for the SWM4-NDP model?Thank you for taking the time to read this email. I would be more than happy to provide further details if needed.Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with: Shell particles are not implemented with domain decomposition
Dear gromacs users,Has anyone experienced a problem with running polarisable water model SWM4-NDP with the following warning:Shell particles are not implemented with domain decomposition?The md.log also stated the following: Number of hardware threads detected (12) does not match the number reported by OpenMP (1). I don't think this is the cause, as this message was also found in my other "working" calculations.I have tried using OpenMP and also tried a variety of -ntmpi and -ntomp settings.The same calculation did not work in GROMACS versions 5.0 and 5.0.1, in the following cluster:Gromacs version: VERSION 5.0.1Precision: doubleMemory model:64 bitMPI library:MPIOpenMP support: enabledGPU support:disabledinvsqrt routine: gmx_software_invsqrt(x)SIMD instructions: NONEFFT library:fftw-3.3.3RDTSCP usage:disabledC++11 compilation: disabledTNG support:enabledTracing support: disabledBuilt on: Thu Sep 18 20:14:41 KST 2014Built by: r...@master.hpc [CMAKE]Build OS/arch: Linux 2.6.18-274.7.1.el5 x86_64Build CPU vendor: GenuineIntelBuild CPU brand: Intel(R) Xeon(R) CPU X3220 @ 2.40GHzBuild CPU family: 6 Model: 15 Stepping: 11Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 ssse3C compiler: /usr/bin/cc GNU 4.1.2C compiler flags: -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUGC++ compiler:/usr/bin/c++ GNU 4.1.2C++ compiler flags: -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUGBoost version: 1.55.0 (internal)Using 24 MPI processesUsing 1 OpenMP thread per MPI processHowever, the same input files worked in another cluster (albeit very slowly, ~0.3ns/day).Gromacs version: VERSION 5.0Precision: singleMemory model:64 bitMPI library:MPIOpenMP support: enabledGPU support:disabledinvsqrt routine: gmx_software_invsqrt(x)SIMD instructions: AVX_256FFT library:fftpack (built-in)RDTSCP usage:enabledC++11 compilation: disabledTNG support:enabledTracing support: disabledBuilt on: Thu Aug 28 16:44:08 KST 2014Built by: root@kant [CMAKE]Build OS/arch: Linux 2.6.32-431.23.3.el6.x86_64 x86_64Build CPU vendor: GenuineIntelBuild CPU brand: Intel(R) Core(TM) i5-4670 CPU @ 3.40GHzBuild CPU family: 6 Model: 60 Stepping: 3Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apicC compiler: /usr/bin/gcc GNU 4.4.7C compiler flags: -mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUGC++ compiler:/usr/bin/g++ GNU 4.4.7C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUGBoost version: 1.55.0 (internal)Using 1 MPI processUsing 16 OpenMP threadsRegards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with: Shell particles are not implemented with domain de
Dear David, Justin, Mark and all,Many thanks for your feedback, that really helped clarify a lot of the questions I had.- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 9월 18일(목) 21:26:41제목 : Re: [gmx-users] Problem with: Shell particles are not implemented with domain deOn 9/18/14 8:01 AM, Kester Wong wrote: Dear gromacs users, Has anyone experienced a problem with running polarisable water model SWM4-NDP with the following warning: Shell particles are not implemented with domain decomposition? Out of curiosity, what is the source of your SWM4-NDP topology? I obtained the SWM4-NDP code from virtualchemistry.org. The md.log also stated the following: Number of hardware threads detected (12) does not match the number reported by OpenMP (1). I don't think this is the cause, as this message was also found in my other "working" calculations. I have tried using OpenMP and also tried a variety of -ntmpi and -ntomp settings. The only valid option here is -ntmpi 1 and -ntomp equal to whatever number of cores you're using. Until I finish the DD implementation for shells/Drudes, only OpenMP is supported here.-Justin Say for example, if I allocate 24 CPUs over 2 nodes (knowing that the calculation would only run on one domain), then theoretically speaking the valid setting should be -ntmpi 24 and -ntomp 1?In the cases of (-ntmpi 24 -ntomp 1) and (-ntmpi 1 -ntomp 1), the resulting Fatal error says: Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPIDo you have a ballpark estimate on when will the support for DD will be made available? I am more than happy to be the first one using/testing it. The same calculation did not work in GROMACS versions 5.0 and 5.0.1, in the following cluster: Gromacs version:VERSION 5.0.1 Precision: double Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: NONE FFT library:fftw-3.3.3 RDTSCP usage: disabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Sep 18 20:14:41 KST 2014 Built by: r...@master.hpc [CMAKE] Build OS/arch: Linux 2.6.18-274.7.1.el5 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU X3220 @ 2.40GHz Build CPU family: 6 Model: 15 Stepping: 11 Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 ssse3 C compiler: /usr/bin/cc GNU 4.1.2 C compiler flags: -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.1.2 C++ compiler flags:-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG Boost version: 1.55.0 (internal) Using 24 MPI processes Using 1 OpenMP thread per MPI process However, the same input files worked in another cluster (albeit very slowly, ~0.3ns/day). Gromacs version:VERSION 5.0 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX_256 FFT library:fftpack (built-in) RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Aug 28 16:44:08 KST 2014 Built by: root@kant [CMAKE] Build OS/arch: Linux 2.6.32-431.23.3.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-4670 CPU @ 3.40GHz Build CPU family: 6 Model: 60 Stepping: 3 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU 4.4.7 C compiler flags:-mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/g++ GNU 4.4.7 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) Using 1 MPI process Using
Re: [gmx-users] Problem with: Shell particles are not implemented with domain de
Hi Mark,Thanks for your reply email.- 원본 메일 -보낸사람 : Mark Abraham mark.j.abra...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2014년 9월 18일(목) 21:26:48제목 : Re: [gmx-users] Problem with: Shell particles are not implemented with domain deOn Thu, Sep 18, 2014 at 2:01 PM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear gromacs users, Has anyone experienced a problem with running polarisable water model SWM4-NDP with the following warning: Shell particles are not implemented with domain decomposition? That means what it says - you can't have more than one domain, which means you can't use more than one MPI rank. Hopefully OpenMP will work to let you use more than one core, but such code paths got very little love in the years leading up to 5.0 The md.log also stated the following: Number of hardware threads detected (12) does not match the number reported by OpenMP (1). I don't think this is the cause, as this message was also found in my other "working" calculations. That suggests something is broken somewhere, but you're using prehistoric compilers, so you're clearly not after high performance in the first place ;-) MarkSuppose I replace the compiler with a more recent one, e.g. 4.9.1 or 4.7.4, will it enable the calculation on one MPI rank at least?Could you please advise if there is any other aspect of tweaks that I can do to improve my clusters' performance?Since the Drude/shell system would only work on one domain, would it be wise to set the OpenMP to lesser than 16?I thought the higher number of OpenMP thread used (say for example -ntomp 16), the more time we will lose for it becomes less efficient?Cheers,Kester<kester2...@ibs.re.kr><kester2...@ibs.re.kr><kester2...@ibs.re.kr> I have tried using OpenMP and also tried a variety of -ntmpi and -ntomp settings. The same calculation did not work in GROMACS versions 5.0 and 5.0.1, in the following cluster: Gromacs version:VERSION 5.0.1 Precision: double Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: NONE FFT library:fftw-3.3.3 RDTSCP usage: disabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Sep 18 20:14:41 KST 2014 Built by: r...@master.hpc [CMAKE] Build OS/arch: Linux 2.6.18-274.7.1.el5 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU X3220 @ 2.40GHz Build CPU family: 6 Model: 15 Stepping: 11 Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 ssse3 C compiler: /usr/bin/cc GNU 4.1.2 C compiler flags: -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.1.2 C++ compiler flags:-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG Boost version: 1.55.0 (internal) Using 24 MPI processes Using 1 OpenMP thread per MPI process However, the same input files worked in another cluster (albeit very slowly, ~0.3ns/day). Gromacs version:VERSION 5.0 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX_256 FFT library:fftpack (built-in) RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Aug 28 16:44:08 KST 2014 Built by: root@kant [CMAKE] Build OS/arch: Linux 2.6.32-431.23.3.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-4670 CPU @ 3.40GHz Build CPU family: 6 Model: 60 Stepping: 3 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU 4.4.7 C compiler flags:-mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/g++ GNU 4.4.7 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-
Re: [gmx-users] Problem with: Shell particles are not implemented with domain de
Dear David,Thanks for the reply! I was wondering if you have had the same issue with this force field, such that you could only use one domain for all the SWM4-NDP calculations?Knowing that I could only use one MPI rank, is there a way to get the calculation work on two nodes? One of my systems has 10k water molecules :(Regards,Kester- 원본 메일 -보낸사람 : David van der Spoel sp...@xray.bmc.uu.se받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 9월 19일(금) 02:11:26제목 : Re: [gmx-users] Problem with: Shell particles are not implemented with domain deOn 2014-09-18 14:26, Justin Lemkul wrote: On 9/18/14 8:01 AM, Kester Wong wrote: Dear gromacs users, Has anyone experienced a problem with running polarisable water model SWM4-NDP with the following warning: Shell particles are not implemented with domain decomposition? Out of curiosity, what is the source of your SWM4-NDP topology? http://virtualchemistry.org/pol.php The md.log also stated the following: Number of hardware threads detected (12) does not match the number reported by OpenMP (1). I don't think this is the cause, as this message was also found in my other "working" calculations. I have tried using OpenMP and also tried a variety of -ntmpi and -ntomp settings. The only valid option here is -ntmpi 1 and -ntomp equal to whatever number of cores you're using. Until I finish the DD implementation for shells/Drudes, only OpenMP is supported here. -Justin The same calculation did not work in GROMACS versions 5.0 and 5.0.1, in the following cluster: Gromacs version:VERSION 5.0.1 Precision: double Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: NONE FFT library:fftw-3.3.3 RDTSCP usage: disabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Sep 18 20:14:41 KST 2014 Built by: r...@master.hpc [CMAKE] Build OS/arch: Linux 2.6.18-274.7.1.el5 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU X3220 @ 2.40GHz Build CPU family: 6 Model: 15 Stepping: 11 Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 ssse3 C compiler: /usr/bin/cc GNU 4.1.2 C compiler flags: -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.1.2 C++ compiler flags:-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG Boost version: 1.55.0 (internal) Using 24 MPI processes Using 1 OpenMP thread per MPI process However, the same input files worked in another cluster (albeit very slowly, ~0.3ns/day). Gromacs version:VERSION 5.0 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX_256 FFT library:fftpack (built-in) RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Aug 28 16:44:08 KST 2014 Built by: root@kant [CMAKE] Build OS/arch: Linux 2.6.32-431.23.3.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-4670 CPU @ 3.40GHz Build CPU family: 6 Model: 60 Stepping: 3 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc GNU 4.4.7 C compiler flags:-mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/g++ GNU 4.4.7 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) Using 1 MPI process Using 16 OpenMP threads Regards, Kester -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding
Re: [gmx-users] Converting TIPS3P model to SWM4-NDP model
That would be great Justin, I look forward to using the new Drude tool.I have registered but could not upload a file to the User Contribution page.Cheers,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 9월 17일(수) 20:35:20제목 : Re: [gmx-users] Converting TIPS3P model to SWM4-NDP model On 9/16/14 9:15 PM, Kester Wong wrote: Dear Justin, Thank you for the feedback. Yep, the converted structure is not any better than a starting configuration, i.e. discontinued ensemble velocitites and another energy minimisation for the converted structure is necessary. What I thought would be helpful is that for water droplet formation, users might save a couple of nanoseconds by having a droplet starting file, instead of a water box. Anyone is welcome to contribute whatever they feel is useful in the User Contributions section of the website. Conversions between polarizable and nonpolarizable models will be trivial when my Drude branch is ready to be merged into the main code repository, so the need for any hacks is very low. Soon it will be possible to very easily do full biomolecular simulations with polarizable force fields just as one would with additive models (i.e., pdb2gmx will build everything for you). There are a few lingering issues that I'm sorting out, but it should be done fairly soon. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Converting TIPS3P model to SWM4-NDP model
Dear gromacs team,I have recently converted a TIPS3P system (10k molecules) to a SWM4-NDP model.As I followed the instruction as listed below, I find it hard for beginners like me to convert the water structure:http://www.gromacs.org/Documentation/How-tos/Changing_a_3_Point_Water_Model_to_a_4_Point_Water_ModelNotwithstanding, after doing some reading and tinkering on the .gro file formatting, and tinkering, I have managed to convert TIPS3P water to SWM4-NDP models.I find this technique very useful, as I think I could probably save some computing time by having the first few ns of the equilibration of SWM4-NDP model done in a less expensive way (e.g. 3-point water model). It can be applied for other water models too, e.g. TIP3P to TIP4P and TIP5P conversions.I have devised a short step-by-step note that I think might be useful to other gromacs users. This could also be a good opportunity to update the web page with more information?Please let me know if this is okay, and I will send the notes as a doc. attachment?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Converting TIPS3P model to SWM4-NDP model
Dear Justin,Thank you for the feedback. Yep, the converted structure is not any better than a starting configuration, i.e. discontinued ensemble velocitites and another energy minimisation for the converted structure is necessary.What I thought would be helpful is that for water droplet formation, users might save a couple of nanoseconds by having a droplet starting file, instead of a water box.Cheers,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 9월 17일(수) 02:29:13제목 : Re: [gmx-users] Converting TIPS3P model to SWM4-NDP model On 9/16/14 4:48 AM, Kester Wong wrote: Dear gromacs team, I have recently converted a TIPS3P system (10k molecules) to a SWM4-NDP model. As I followed the instruction as listed below, I find it hard for beginners like me to convert the water structure: http://www.gromacs.org/Documentation/How-tos/Changing_a_3_Point_Water_Model_to_a_4_Point_Water_Model Notwithstanding, after doing some reading and tinkering on the .gro file formatting, and tinkering, I have managed to convert TIPS3P water to SWM4-NDP models. I find this technique very useful, as I think I could probably save some computing time by having the first few ns of the equilibration of SWM4-NDP model done in a less expensive way (e.g. 3-point water model). It can be applied for other water models too, e.g. TIP3P to TIP4P and TIP5P conversions. I don't know that there's much to gain by doing such conversions. You still have to re-equilibrate no matter what, and the choice of TIP3P-equilibrated configuration is arbitrary; the final configuration of the simulation is not necessarily any better than any other snapshot, and you lose any semblance of continuity because you can't preserve the equilibrated ensemble of velocities, etc. -Justin I have devised a short step-by-step note that I think might be useful to other gromacs users. This could also be a good opportunity to update the web page with more information? Please let me know if this is okay, and I will send the notes as a doc. attachment? Regards, Kester -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Contact angle measurement on a flat surface
Hi Mark,Thank you for the information, that helps a lot!Binning the density profile seems to be the method of choice in quite a large number of papers published.Perhaps this method could be made into a GROMACS utility tool for future use? Thanks again Mark.Regards,Kester- 원본 메일 -보낸사람 : Mark Abraham mark.j.abra...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2014년 9월 11일(목) 21:25:09제목 : Re: [gmx-users] Contact angle measurement on a flat surfaceHi, Petter Johanson here in Berk's group does some similar things in a fairly ad-hoc way (bin the density profile), but he suggests the methods here http://www.mdpi.com/1099-4300/15/9/3734 might be useful. Mark On Wed, Sep 10, 2014 at 5:45 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear all, I would like to know what are the methods I could use to measure/plot the contact angle of a water nanodroplet on flat graphene. Is there a script or tool in GROMACS that can perform the contact angle calculation? I am aware that the commonly used Young's equation does not apply here, since the droplet sizes will be in nanoscale. The modified Young-Dupre's equation, and other plotting methods such as the graphical binning approach by Werder et al. J. Phys. Chem. B 107, 1345-1352 (2003), and the algorithm method by Ingebrigtsen and Toxvaerd, J. Phys. Chem. C 111, 8518 (2007) provided some theory on the calculation, but I would like to know about the technical steps on doing the measurement. Any feedback is greatly appreciated. Thank you in advance. Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Contact angle measurement on a flat surface
Dear all,I would like to know what are the methods I could use to measure/plot the contact angle of a water nanodroplet on flat graphene.Is there a script or tool in GROMACS that can perform the contact angle calculation? I am aware that the commonly used Young's equation does not apply here, since the droplet sizes will be in nanoscale.The modified Young-Dupre's equation, and other plotting methods such as the graphical binning approach by Werder et al. J. Phys. Chem. B 107, 1345-1352 (2003), and the algorithm method by Ingebrigtsen and Toxvaerd, J. Phys. Chem. C 111, 8518 (2007) provided some theory on the calculation, but I would like to know about the technical steps on doing the measurement.Any feedback is greatly appreciated.Thank you in advance.Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Unrealistic behaviour of water on graphene [NVT]
Hi Tsjerk, Do you have experimental data on the behaviour of 2000 or 6000 or 1 water molecules on a sheet of graphene? There are experimental and theoretical data that describe the contact angle of water on graphene. Current experimental data of water droplets on a sheet of graphene can be found in the work byRafiee et al., Nature Materials Vol. 11 217-222 (2012), Li et al., Nature Materials Vol. 12 925-931(2013), and Zhou et al., Phys. Rev. B 85, 035406 (2012).Theoretical calculations of the 2000, 6000, and 10,000 molecules have also been reported by Shih et al., Nature Materials (Commentary) Vol. 12 866-869 (2013),Shih et al., PRL 109, 176101 (2012),and Taherian et al., Langmuir 29, 1457-1465 (2013), just to name a few. Do you _know_ it's wrong behaviour?Since I am new to gromacs calculations, I am afraid I do not know what went wrong with the calculation. Either the effect of polarisation makes the surface superhydrophilic, or the neighbouring interaction prevents water from forming a droplet.Water should, however, form a droplet on the surface. If yes, then, given that the water forms a droplet in vacuum, even if above the graphene sheet, you know the water behaviour itself is sort of correct. I would be most suspicious of the water-graphene interactions. Where did those parameters come from?GRAPPA force field (Hughes et al., Nanoscale 6, 5438-5448 (2014)) was developed based on CHARMM FF, where the FF parameters were obtained through first deriving a set of C-C parameters, following by the parameters of different oxygen-containing species.Another similar polarisable FF was also recently developed based on OPLS/AA by Schyman and Jorgensen, J. Phys. Chem. Lett. 4, 468-474 (2013). Do they account for increased electron density above the plane because of all the pi-orbitals?I am not absolutely certain that the pi-orbitals were accounted for, however, the authors have described that GRAPPA can capture the overlap of pi-electron cloud between residue and graphene surface.Regards,Kester Do you have experimental data on the behaviour of 2000 or 6000 or 1 water molecules on a sheet of graphene? Do you _know_ it's wrong behaviour? If yes, then, given that the water forms a droplet in vacuum, even if above the graphene sheet, you know the water behaviour itself is sort of correct. I would be most suspicious of the water-graphene interactions. Where did those parameters come from? Do they account for increased electron density above the plane because of all the pi-orbitals? Cheers, Tsjerk On Tue, Sep 2, 2014 at 8:24 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear gmx-users, I am modelling a water droplet using a water box model, and have encountered unrealistic behaviour of equilibrating water on graphene, using GRAPPA force field in GROMACS 5.0. The box size is about 30x30x15 nm. Structure-wise, the water models (2000, 6000, and 10,000 water molecules) appear to be spreading like a flat layer of solution, rather than a droplet. Additionally, for the 10,000 molecules on graphene, water droplet was formed in vacuo above the surface. I have posted some questions on GROMACS user list, however, I have yet to receive any feedback. Could anyone please look at my .mdp parameter and the .xtc trajectory files? I do not know what caused the spreading of water on graphene. There are two parameter settings that I have used, they are labeled as lincs-order=4 (larger temperature constant and time-step), and lincs-order=8 (smaller temperature constant and time-step). The starting configuration (pdb), trajectories (xtc), and parameter (mdp) files are uploaded in my Google Drive: https://drive.google.com/folderview?id=0B7ym8d6G9-e2Tlh4VGNSaDhCbmcusp=sharing https://drive.google.com/folderview?id=0B7ym8d6G9-e2Rl9WaXNrUlVRa28usp=sharing https://drive.google.com/folderview?id=0B7ym8d6G9-e2bnFzbWN3VHVqbE0usp=sharing Please let me know if you need more information/files on the GRAPPA-based calculations. Any help will be tremendously appreciated. Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the a
[gmx-users] Creating an ITP file for charmm27
Dear gmx-users,I have manually created a graphene.itp file for charmm27 forcefield calculations, with the intention to model the contact angle of water.The atomic mass and charge values were obtained from the forcefield ffnonbonded.itp.Could anyone please advise if my file is correct?[ moleculetype ];name nrexclGRA 3[ atoms ]; id at type resnum resname atname cg no charge mass 1 C 1 GRA C 1 0.51 12.011 2 C 1 GRA C 2 0.51 12.011 3 C 1 GRA C 3 0.51 12.011 4 C 1 GRA C 4 0.51 12.011 5 C 1 GRA C 5 0.51 12.011 6 C 1 GRA C 6 0.51 12.011 7 C 1 GRA C 7 0.51 12.011 8 C 1 GRA C 8 0.51 12.011 9 C 1 GRA C 9 0.51 12.011 10 C 1 GRA C 10 0.51 12.011 11 C 1 GRA C 11 0.51 12.011 12 C 1 GRA C 12 0.51 12.011 13 C 1 GRA C 13 0.51 12.011 14 C 1 GRA C 14 0.51 12.011 15 C 1 GRA C 15 0.51 12.011 16 C 1 GRA C 16 0.51 12.011 17 C 1 GRA C 17 0.51 12.011 18 C 1 GRA C 18 0.51 12.011 19 C 1 GRA C 19 0.51 12.011 20 C 1 GRA C 20 0.51 12.011 21 C 1 GRA C 21 0.51 12.011 22 C 1 GRA C 22 0.51 12.011 23 C 1 GRA C 23 0.51 12.011 24 C 1 GRA C 24 0.51 12.011 25 C 1 GRA C 25 0.51 12.011 26 C 1 GRA C 26 0.51 12.011 27 C 1 GRA C 27 0.51 12.011 28 C 1 GRA C 28 0.51 12.011 29 C 1 GRA C 29 0.51 12.011 30 C 1 GRA C 30 0.51 12.011 31 C 1 GRA C 31 0.51 12.011 32 C 1 GRA C 32 0.51 12.011 33 C 1 GRA C 33 0.51 12.011 34 C 1 GRA C 34 0.51 12.011 35 C 1 GRA C 35 0.51 12.011 36 C 1 GRA C 36 0.51 12.011 37 C 1 GRA C 37 0.51 12.011 38 C 1 GRA C 38 0.51 12.011 39 C 1 GRA C 39 0.51 12.011 40 C 1 GRA C 40 0.51 12.011 41 C 1 GRA C 41 0.51 12.011 42 C 1 GRA C 42 0.51 12.011 43 C 1 GRA C 43 0.51 12.011 44 C 1 GRA C 44 0.51 12.011 45 C 1 GRA C 45 0.51 12.011 46 C 1 GRA C 46 0.51 12.011 47 C 1 GRA C 47 0.51 12.011 48 C 1 GRA C 48 0.51 12.011 49 C 1 GRA C 49 0.51 12.011 50 C 1 GRA C 50 0.51 12.011 51 C 1 GRA C 51 0.51 12.011 52 C 1 GRA C 52 0.51 12.011 53 C 1 GRA C 53 0.51 12.011 54 C 1 GRA C 54 0.51 12.011 55 C 1 GRA C 55 0.51 12.011 56 C 1 GRA C 56 0.51 12.011 57 C 1 GRA C 57 0.51 12.011 58 C 1 GRA C 58 0.51 12.011 59 C 1 GRA C 59 0.51 12.011 60 C 1 GRA C 60 0.51 12.011In the tutorial by Andrea Minoia (http://chembytes.wikidot.com/grocnt), all the charges of graphene were set to zero, but I have decided to keep the graphene surface charges.Has anyone looked at the difference between the water/graphene interaction, having a charged graphene .itp file as opposed to zero charge itp?When creating the tpr file for energy minimisation:gmx_mpi grompp -f em.mdp -c graphene_.gro -n system.ndx -o topol.tprI received this:System has non-zero total charge: 30.5944.Total charge should normally be an integer.Will the partial charge of graphene affect the NVT run, apart from slowing it down?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Water droplet moving away from surface
Dear all,I am running an equilibration calculation using a new force field (GRAPPA), for a 10,000 water molecules on graphene. The run is up to 378 ps now. Iam concerned that the water droplet will drift away from the surface, rather than forming a nice droplet.Is the cutoff values in my equilibration setup appropriate for this water/graphene in vacuum?I have shared the link to the XTC, PDB, and MDP files for my run.https://drive.google.com/file/d/0B7ym8d6G9-e2eUJQMDFLTlBBZ1U/edit?usp=sharingRegards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to setup my PBS script?
Dear all,I think my PBS job script is not appropriate.I would like to knowhow to optimise my equilibration rate on two nodes?The specs of the cluster I am using is as follows:Linux master.hpc 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 16:21:01 EDT 2011 x86_64 x86_64 x86_64 GNU/LinuxThe CPU information of my cluster is:Intel(R) Xeon(R) CPU X3220 = Processor composition =Processors(CPUs) : 4Packages(sockets) : 1Cores per package : 4Threads per core : 1= Processor identification =ProcessorThread Id. Core Id.Package Id.0000 1020 2010 3030 = Placement on packages =Package Id. Core Id.Processors00,2,1,3 0,1,2,3= Cache sharing =Cache Size ProcessorsL1 32 KB no sharingL2 4 MB (0,2)(1,3)My pestat with job ID 29515 (38400 atoms) and 29513 (102576 atoms): node state load pmem ncpu mem resi usrs tasks jobids/users x001 excl 11.99 32114 12 35934 833 16/2 12 29503 DBS x002 excl 12.03 32114 12 35934 2303 3/2 12 29505 HYV x003 excl 0.00* 32114 12 35934 219 0/0 12 29515 Kester x004 excl 11.87 32114 12 35934 727 16/1 12 29506 NJP x005 excl 0.00* 32114 12 35934 188 0/0 12 29513 Kester x006 excl 11.99 64386 12 68206 2309 6/2 12 29508 HYV x007 excl 12.00 64383 12 68203 1125 8/2 12 29418 DBS x008 excl 0.99* 32111 12 35931 479 7/2 12 29513 Kester x009 excl 0.99* 32111 12 35931 286 1/1 12 29515 KesterI am concerned about the "load" as pestat shows 0.00* for my jobs running on dual nodes. When running on one node, the load was showing 0.99*, which I think is not running at full capability?I am aware that the current installation runs on SSE2, while the log file generated by the NVT run suggested using SSE4.1.Also, with regardf to the domain decomposition flag in the PBS run script,the effect/performance should be the same with or without domain decomposition being specified, as the mdrun would guesstimate one for the job?This is the job script that I use:#!/bin/bash#PBS -l nodes=2:west:ppn=12#PBS -l ncpus=24#PBS -l walltime=10:00:00#PBS -N NVTNPROCS=`wc -l $PBS_NODEFILE`hostnamedategromacs="/usr/local/gromacs/share/gromacs/top/gmx_mpi mdrun -s topol.tpr -cpi state.cpt"cd $PBS_O_WORKDIRcp $PBS_NODEFILE nodefilegmx_mpi mdrun -s topol.tpr -cpi state.cptI have been unable to get help from my research group as I am the only one that uses GROMACS, and I am new to this too.Searching on Google and GROMACS mail list brought little help as there are so many different types of PCs.Any advice is greatly appreciated, thanks in advance!Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
Dear Lovika,Have you looked into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue?Regards,Kester- 원본 메일 -보낸사람 : Lovika Moudgil lovikamoud...@gmail.com받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 24일(일) 18:28:06제목 : [gmx-users] mdrun errorHi everyone , Need some help .I have got an error in my mdrun . Upto grompp every thing was fine but when I give command for mdrun ,It stops with this ... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=1 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, atom= 19 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.0853354e+18 Maximum force =inf on atom 19 Norm of force = 1.7429674e+18 constraints are all ready none ...Please help me what should I do to solve this . Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error
If the H-atom is constituent of a molecule (e.g. H2O), then you could also try moving the molecule coordinates and see how it goes.I had a similar issue, but moving the molecule by an angstrom worked in my case. Good luck!Regards,Kester- 원본 메일 -보낸사람 : Lovika Moudgil lovikamoud...@gmail.com받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 25일(월) 13:52:49제목 : Re: [gmx-users] mdrun errorThanks for reply Justin and Kester...Ya my geometry is getting distorted and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the error is same Regards Lovika On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong <kester2...@ibs.re.kr> wrote: Dear Lovika, Have you looked into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue? Regards, Kester - 원본 메일 - *보낸사람* : Lovika Moudgil <lovikamoud...@gmail.com> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 8월 24일(일) 18:28:06 *제목* : [gmx-users] mdrun error Hi everyone , Need some help .I have got an error in my mdrun . Upto grompp every thing was fine but when I give command for mdrun ,It stops with this ... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=1 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, atom= 19 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.0853354e+18 Maximum force =inf on atom 19 Norm of force = 1.7429674e+18 constraints are all ready none ...Please help me what should I do to solve this . Thanks and Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulating different pH values of water
Hi Tsjerk,Thanks for your reply. I want to study the effect of pH on the wetting behaviour of water nanodroplet on graphene, the contact angle especially.For acidic solution, H and Cl ions are included in the water model, whereas for a high pH solution, there will be Na and OH ions, for instance.I am aware that a lot of quantum mechanics studies have been put into obtaining the H2O-carbon interaction properties with MP2 level accuracy.Using polarisable force field in this case might capture the properties of the charged ions, however, I am concerned if this approach is appropriate.Any feedback is greatly appreciated.Regards,Kester- 원본 메일 -보낸사람 : Tsjerk Wassenaar tsje...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2014년 8월 21일(목) 14:37:55제목 : Re: [gmx-users] Simulating different pH values of waterHi Kester, You do realize that water is odd quantum stuff, with oxygens going about in a sea of protons? The main way to move a free proton is to rewire the O-H bonds. What effects do you want investigate with your simulations? That determines what setup you need. Cheers, Tsjerk On Aug 21, 2014 6:46 AM, "Kester Wong" <kester2...@ibs.re.kr> wrote: Dear all, This might not be relevant to MD technicalities, but I guess I should give it a shot. I would like to simulate water droplets at different pH values. However, knowing that a realistic system would need 180k water molecules to mimic a pH of 7. Is there another viable approach that I can use to simulate water droplets from low to high pH values? The original question was posted here: https://www.researchgate.net/post/How_can_I_calculate_the_number_of_molecules_with_respect_to_the_pH-value_in_solution?_tpcectx=subscription_feed#53f576d7d4c11805568b469c Regards, Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simulating different pH values of water
Dear all,This might not be relevant to MD technicalities, but I guess I should give it a shot. I would like to simulate water droplets at different pH values. However, knowing that a realistic system would need 180k water molecules to mimic a pH of 7.Is there another viable approach that I can use to simulate water droplets from low to high pH values?The original question was posted here:https://www.researchgate.net/post/How_can_I_calculate_the_number_of_molecules_with_respect_to_the_pH-value_in_solution?_tpcectx=subscription_feed#53f576d7d4c11805568b469cRegards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Hi Justin,After some googling, and tweaking with the mdp parameters (step size), I think I have managed to produce the ener.edr and ultimately the ener.xvg files.Anyway, the same problem occured at the same atom each time after an energy minimisation calculation, pointing at the same atom, irregardless of my "emstep".So, I went to my structure(.gro) file and made some changes to the problematic atom (atom 33772) by moving the atomic coordinates of 33772, 33773 and 33774 along the z-direction. I did that because the atom belongs to a water molecule.After that, the "ndx" and "tpr" files were updated.The subsequent energy minimisation based on the amended "gro" file fixed the issue, albeit with further corrections to other atoms/molecules.The confout.gro and ener.edr files were then produced alright.Kester----- 원본 메일 -보낸사람 : Kester Wong kester2...@ibs.re.kr받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 11:57:30제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?Hi Justin,I think I might have used a pretty small Fmax value for my system of 2000+ water molecules.The md.log file reports:Steepest Descents converged to machine precision in 14 steps,but did not reach the requested Fmax 200.Potential Energy = 7.9771407e+19Maximum force = inf on atom 33772Norm of force = infI guess this issue would be corrected using emtol = 1000?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 01:44:08제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?On 8/18/14, 8:15 AM, Kester Wong wrote: Hi Justin, THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine. Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation. For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files. Are sensible energies reported in the corresponding .log file? A run may "finish" but yield infinite energies if something failed. That can also lead to an incorrect interpretation of .edr contents. Again, running gmxcheck on all output files can be useful here. -Justin Regards, Kester - 원본 메일 - *보낸사람* : Justin Lemkul <jalem...@vt.edu> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 8월 18일(월) 20:56:56 *제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility
[gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Dear all,After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file.However, of all the energy minimised structures I have, one did not work.I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvgAs the same procedure worked for all my other structures, this fatal error read:Program g_energy_mpi, VERSION 5.0Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822Fatal error:Energy file ener.edr not recognized, maybe different CPU?The xvg file was successfully produced for other structures, why did it fail on this particular system?Regards,Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Hi Justin,THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine.Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation.For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files.Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 18일(월) 20:56:56제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?
Hi Justin,I think I might have used a pretty small Fmax value for my system of 2000+ water molecules.The md.log file reports:Steepest Descents converged to machine precision in 14 steps,but did not reach the requested Fmax 200.Potential Energy = 7.9771407e+19Maximum force = inf on atom 33772Norm of force = infI guess this issue would be corrected using emtol = 1000?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul jalem...@vt.edu받는사람 : gmx-us...@gromacs.org받은날짜 : 2014년 8월 19일(화) 01:44:08제목 : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 8:15 AM, Kester Wong wrote: Hi Justin, THanks for the quick reply. I am concerned that it might be the ener.edr file that is fragmented, as the md.log report seem fine. Also, the same problem persisted even when the input files were migrated to a new folder for an energy minimisation calculation. For the second energy minimisation calculation, I even re-generated the system.ndx and topol.tpr files. Are sensible energies reported in the corresponding .log file? A run may "finish" but yield infinite energies if something failed. That can also lead to an incorrect interpretation of .edr contents. Again, running gmxcheck on all output files can be useful here. -Justin Regards, Kester - 원본 메일 - *보낸사람* : Justin Lemkul <jalem...@vt.edu> *받는사람* : <gmx-us...@gromacs.org> *받은날짜* : 2014년 8월 18일(월) 20:56:56 *제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU? On 8/18/14, 7:43 AM, Kester Wong wrote: Dear all, After the energy minimisation calculation, I plotted the (energy vs time) profile for some structures with the ener.xvg file. However, of all the energy minimised structures I have, one did not work. I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg" using the command: g_energy_mpi -f ener.edr -o ener.xvg As the same procedure worked for all my other structures, this fatal error read: Program g_energy_mpi, VERSION 5.0 Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c, line: 822 Fatal error: Energy file ener.edr not recognized, maybe different CPU? The xvg file was successfully produced for other structures, why did it fail on this particular system? Investigate the .log file and run gmxcheck on all of the output files of the problematic run. Likely it failed and produced fragmented output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to record log file?
text/html; charset=UTF-8: Unrecognized -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Command not found after typing g_luck
Dear all,I am a new GROMACS user. I have recently installed GROMACS 5.0 on Intel(R) Xeon(R) CPU X3220 withx86_64 architecture. Installation went without a problem, but I could not seem to get anything from the "g_luck" command.Also, I could not find the g_luck_mpi in my/usr/local/gromacs/bin directory.Another problem is that, when I typed echo $SHELL, I get /bin/bash.As I try to to change bash to csh, by tying "csh", I am still getting/bin/bash.What should I do?Kester -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
