[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.
[gmx-users] van hove correlation function
Hi, I have calculated van hove correlation function of lipids using g_vanhove tool. Now I want to calculate the non gaussian parameter of this function which is defined as: α2(*t*) = 3 [image: left angle bracket]*r*4(*t*) [image: right angle bracket]/5 [image: left angle bracket]*r*2(*t*) [image: right angle bracket] 2 – 1 where [image: left angle bracket]*r*2(*t*) [image: right angle bracket] is the MSD. But the problem is that MSD is directly calculated from the g_msd tool, so how to calculate [image: left angle bracket]*r*4(*t*) [image: right angle bracket] from MSD? And if there is any way to calcualte this parameter directly from the g_vanhove tool? Please help. -- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 79 -- 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 define the center of mass for a droplet consisting of different ions and molecules?
On 3/3/15 5:59 AM, Kester Wong wrote: 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 57SOLHW1 36290 17.602 14.916 0.487 57SOLHW2 36291 17.571 14.843 0.615 58SOL OW 36292 17.588 14.547 0.457 58SOLHW1 36293 17.573 14.642 0.458 58SOLHW2 36294 17.521 14.512 0.516 59SOL OW 36295 11.747 17.611 1.159 59SOLHW1 36296 11.714 17.522 1.174 59SOLHW2 36297 11.740 17.624 1.064 To 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; end Then, 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? Look at the code for gmx traj. It does these calculations with gmx traj -ox -com. Save some time and use existing software rather than reinventing the wheel :) -Justin Below is an example of the coordinate file: 2015SOL OW 42163 17.143 16.975 0.502 2015SOLHW1 42164 17.175 17.038 0.567 2015SOLHW2 42165 17.222 16.937 0.464 2016SOL OW 42166 16.088 17.097 0.778 2016SOLHW1 42167 16.094 17.182 0.734 2016SOLHW2 42168 16.159 17.098 0.843 . . . 2035H3O OW 42241 17.895 20.054 0.561 2035H3OH31 42242 17.836 20.100 0.492 2035H3OH32 42243 17.970 20.114 0.593 2035H3OH33 42244 17.930 19.964 0.527 2036H3O OW 42245 13.948 17.327 0.503 2036H3OH31 42246 13.875 17.348 0.571 2036H3OH32 42247 13.978 17.410 0.452 2036H3OH33 42248 14.026 17.276 0.544 . . . 2037CLA CL 42249 13.862 17.882 1.754 2038CLA CL 42250 16.686 17.457 0.667 Thanks in advance. 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 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.
Re: [gmx-users] Appropriate Force Field for Dendrimer-Drug Systems
On 3/3/15 6:49 AM, faride badalkhani wrote: Dear all, I am going to investigate the interaction between poly(amidoamine) dendrimers with different generations, cores, and surface groups (NH2, COOH, OH, etc) and some low soluble drugs such as curcumines and chalcones. So, I should perform a productive MD run on the dendrimer nanostructures and then dock drug into dendrimer and subsequently I should perform a productive MD on dendrimer-drug complexes. But, I couldn't find an appropriate FF for this purpose. What FF in GROMACS do you think can work for me? Since you're going to have to parametrize everything from scratch, any of the force fields can work depending on how straightforward it will be for you to do this work. The time investment here will be considerable and you will need solid target data for validating your new force field. -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.
[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems
So, is it possible for me to use GROMACS package for my project? -- 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] Appropriate Force Field for Dendrimer-Drug Systems
On 3/3/15 8:24 AM, faride badalkhani wrote: So, is it possible for me to use GROMACS package for my project? Of course, but that's just for the simulation or validation itself. Most of the hard work is in deriving the parameters (probably requiring QM, depending on which force field you choose). Putting them in GROMACS format and using them for a simulation is the easy part. -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.
Re: [gmx-users] regarding glycolipids parameters for GROMACS
As usual thanks a lot Justin, i’ll email you asap, Best regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl On March 3, 2015 at 4:00:33 PM, Justin Lemkul (jalem...@vt.edumailto:jalem...@vt.edu) wrote: On 3/3/15 12:36 PM, Carlos Navarro Retamal wrote: Dear gromacs users, I was wondering, are they glycolipids (MGDG more specifically) parameters availably for gromacs package? it doesn’t matter for which forcefield they were constructed. The CHARMM force field should cover all of this, though not in a pre-constructed residue. The parameters should all be there, so it shouldn't be hard to put one together. We're just putting together and testing the glycoprotein and glycolipid force fields (recently converted into GROMACS format) and we'll release them soon, but if you're OK with a beta, email me off-list. -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] high temperature
Hi Justin, That's the .mdp file. dt = 0.0001 tinit = 0 nsteps = 10 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.2 coulombtype = reaction-field-zero epsilon_rf = 0 rcoulomb= 0.1 rvdw= 0.2 vdwtype = cutoff pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 0.1 ref_t = 300 300 tc_grps = CNT water unwanted temperatures from the 2nd computer are: 0.00 569.41912 487.04663 428.94406 548.68127 406.10748 533.70324 487.37088 456.60519 452.93588 442.06088 463.36178 472.95275 502.68411 421.56173 492.36709 537.82879 483.68277 475.07675 494.39749 452.90744 494.20474 474.09298 482.93124 487.88989 509.66070 454.61138 453.75927 460.47540 454.69632 505.48443 485.54705 472.73492 460.27398 493.66903 480.78952 482.55233 470.91381 496.23098 484.82730 455.13006 469.39798 506.39819 479.32211 500.88891 485.77325 489.26815 476.03207 469.77734 466.56793 493.62396 482.78839 470.33157 462.17074 477.09906 470.76757 489.31381 486.11468 475.64276 471.49072 482.00595 485.38873 480.53643 475.79977 469.22253 488.72970 481.01446 493.13934 486.96911 481.62371 469.96023 488.82580 482.96316 476.70632 487.02590 487.53659 476.29904 472.44818 479.97314 477.46865 473.29275 469.93447 474.75863 472.98861 478.05273 486.17233 480.43383 475.78836 482.39563 480.41461 476.73916 490.22122 482.99255 478.54370 480.67889 478.16925 479.58938 474.47232 484.70156 484.90008 481.15057 - wanted temperatures from the 1st computer: 0.00 326.691895 294.764709 298.554596 282.649414 307.463135 291.600189 300.543671 299.999359 297.054443 305.510986 303.078583 299.970428 299.137207 297.810272 298.365875 298.783813 301.805695 303.370575 300.340332 301.656372 299.389984 300.836243 296.977936 298.827637 299.861847 300.578522 296.483398 296.462646 302.666473 297.978180 304.715515 300.773193 300.172913 307.178711 298.444183 312.749542 302.172089 301.957428 303.820526 303.579712 296.149872 296.983826 303.023834 299.992371 299.144897 295.73 305.296722 304.449219 309.249756 302.303375 304.800293 301.949646 302.895538 307.148254 298.277069 302.761719 296.531281 296.709900 298.417542 300.391022 297.293732 299.136353 290.259125 299.269531 305.229675 301.938751 301.106384 301.689117 295.249969 298.655914 296.441071 300.491364 304.039795 301.149384 295.906250 300.652557 296.303467 300.960083 304.725067 291.927765 303.753845 300.202393 294.915588 297.580017 302.882233 300.872406 306.164551 299.459473 300.940948 306.348328 299.031982 299.465942 297.603119 301.168304 305.233917 292.175751 304.453491 300.391571 303.061188 302.262146 Hope they are the data you wanted. Thanks for your time and help. On Tue, Mar 3, 2015 at 10:30 PM, mah maz mahma...@gmail.com wrote: Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the .gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz mahma...@gmail.com wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote: Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz mahma...@gmail.com wrote: Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production
Re: [gmx-users] high temperature
Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the . gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz mahma...@gmail.com wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote: Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz mahma...@gmail.com wrote: Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production step(around 500k). I have changed the mdp file several times but it doesn't work. What are the possible causes of problem? Thank you! dt = 0.0001 tinit = 0 nsteps = 200 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = cut-off rcoulomb= 0.9 rvdw= 0.9 rvdw_switch = 0.5 vdwtype = switch pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 ref_t = 300 tc_grps = CNT gen_temp= 300 pcoupl = no -- 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] high temperature
On 3/3/15 2:00 PM, mah maz wrote: Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the . gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! I'm not prepared to speculate without seeing a full .mdp file and the quantitative evidence of the difference. Guessing wastes your time and mine. -Justin Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz mahma...@gmail.com wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote: Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz mahma...@gmail.com wrote: Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production step(around 500k). I have changed the mdp file several times but it doesn't work. What are the possible causes of problem? Thank you! dt = 0.0001 tinit = 0 nsteps = 200 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = cut-off rcoulomb= 0.9 rvdw= 0.9 rvdw_switch = 0.5 vdwtype = switch pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 ref_t = 300 tc_grps = CNT gen_temp= 300 pcoupl = no -- == 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.
Re: [gmx-users] regarding glycolipids parameters for GROMACS
On 3/3/15 12:36 PM, Carlos Navarro Retamal wrote: Dear gromacs users, I was wondering, are they glycolipids (MGDG more specifically) parameters availably for gromacs package? it doesn’t matter for which forcefield they were constructed. The CHARMM force field should cover all of this, though not in a pre-constructed residue. The parameters should all be there, so it shouldn't be hard to put one together. We're just putting together and testing the glycoprotein and glycolipid force fields (recently converted into GROMACS format) and we'll release them soon, but if you're OK with a beta, email me off-list. -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.
Re: [gmx-users] high temperature
On 3/3/15 2:27 PM, mah maz wrote: Hi Justin, That's the .mdp file. dt = 0.0001 tinit = 0 nsteps = 10 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.2 coulombtype = reaction-field-zero epsilon_rf = 0 rcoulomb= 0.1 rvdw= 0.2 These cutoffs are total nonsense; they are much too short to be physically useful. vdwtype = cutoff pbc = no No PBC in a solvated system? Is this a droplet or is it supposed to be condensed phase? integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 0.1 ref_t = 300 300 tc_grps = CNT water unwanted temperatures from the 2nd computer are: Likely garbage from a physically unreasonable setup. Note that if your temperature is zero at time zero, you're not generating velocities, so you're then letting Nose-Hoover (which oscillates widely) try to make up a huge difference in temperature. Very unlikely to succeed. -Justin 0.00 569.41912 487.04663 428.94406 548.68127 406.10748 533.70324 487.37088 456.60519 452.93588 442.06088 463.36178 472.95275 502.68411 421.56173 492.36709 537.82879 483.68277 475.07675 494.39749 452.90744 494.20474 474.09298 482.93124 487.88989 509.66070 454.61138 453.75927 460.47540 454.69632 505.48443 485.54705 472.73492 460.27398 493.66903 480.78952 482.55233 470.91381 496.23098 484.82730 455.13006 469.39798 506.39819 479.32211 500.88891 485.77325 489.26815 476.03207 469.77734 466.56793 493.62396 482.78839 470.33157 462.17074 477.09906 470.76757 489.31381 486.11468 475.64276 471.49072 482.00595 485.38873 480.53643 475.79977 469.22253 488.72970 481.01446 493.13934 486.96911 481.62371 469.96023 488.82580 482.96316 476.70632 487.02590 487.53659 476.29904 472.44818 479.97314 477.46865 473.29275 469.93447 474.75863 472.98861 478.05273 486.17233 480.43383 475.78836 482.39563 480.41461 476.73916 490.22122 482.99255 478.54370 480.67889 478.16925 479.58938 474.47232 484.70156 484.90008 481.15057 - wanted temperatures from the 1st computer: 0.00 326.691895 294.764709 298.554596 282.649414 307.463135 291.600189 300.543671 299.999359 297.054443 305.510986 303.078583 299.970428 299.137207 297.810272 298.365875 298.783813 301.805695 303.370575 300.340332 301.656372 299.389984 300.836243 296.977936 298.827637 299.861847 300.578522 296.483398 296.462646 302.666473 297.978180 304.715515 300.773193 300.172913 307.178711 298.444183 312.749542 302.172089 301.957428 303.820526 303.579712 296.149872 296.983826 303.023834 299.992371 299.144897 295.73 305.296722 304.449219 309.249756 302.303375 304.800293 301.949646 302.895538 307.148254 298.277069 302.761719 296.531281 296.709900 298.417542 300.391022 297.293732 299.136353 290.259125 299.269531 305.229675 301.938751 301.106384 301.689117 295.249969 298.655914 296.441071 300.491364 304.039795 301.149384 295.906250 300.652557 296.303467 300.960083 304.725067 291.927765 303.753845 300.202393 294.915588 297.580017 302.882233 300.872406 306.164551 299.459473 300.940948 306.348328 299.031982 299.465942 297.603119 301.168304 305.233917 292.175751 304.453491 300.391571 303.061188 302.262146 Hope they are the data you wanted. Thanks for your time and help. On Tue, Mar 3, 2015 at 10:30 PM, mah maz mahma...@gmail.com wrote: Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the .gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz mahma...@gmail.com wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote: Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know
[gmx-users] Running gromacs on Rocks cluster
Dear all,I am running into a problem running gromacs in parallel mode on a rocks cluster using CentOS. When I specify N processors on a single node, it works fine, but when I specify N processors that would require it to span multiple nodes, it runs the same simulation on each node independently rather than having the nodes work together on a single simulation. For installation, I basically followed the procedure here:Compile and run GROMACS 4.5.3 in the Intel® Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 | Intel® Developer Zone | | | | | | | | | Compile and run GROMACS 4.5.3 in the Intel® Cluster Ready Reference Recipe S5520UR-ICR1.1-...In this article I will show you how to compile GROMACS 4.5.3 using the latest Open Source Intel Cluster Ready Reference Design S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 | | | | View on software.intel.com | Preview by Yahoo | | | | | except that I am using gromacs 5.0, open mpi, and CentOS 7 Maybe I need to specify each node (hostname) somehow? I have a feeling that I'm missing something really basic so thanks in advance for whatever help you can offer. LK -- 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] high temperature
On 3/3/15 2:40 PM, mah maz wrote: I see. I just don't understand the difference between these results. Random input settings = random results. MD is chaotic and if you don't have a properly balanced physical setup, you get nonsense. -Justin Useful as always. Many thanks! On Tue, Mar 3, 2015 at 10:57 PM, mah maz mahma...@gmail.com wrote: Hi Justin, That's the .mdp file. dt = 0.0001 tinit = 0 nsteps = 10 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.2 coulombtype = reaction-field-zero epsilon_rf = 0 rcoulomb= 0.1 rvdw= 0.2 vdwtype = cutoff pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 0.1 ref_t = 300 300 tc_grps = CNT water unwanted temperatures from the 2nd computer are: 0.00 569.41912 487.04663 428.94406 548.68127 406.10748 533.70324 487.37088 456.60519 452.93588 442.06088 463.36178 472.95275 502.68411 421.56173 492.36709 537.82879 483.68277 475.07675 494.39749 452.90744 494.20474 474.09298 482.93124 487.88989 509.66070 454.61138 453.75927 460.47540 454.69632 505.48443 485.54705 472.73492 460.27398 493.66903 480.78952 482.55233 470.91381 496.23098 484.82730 455.13006 469.39798 506.39819 479.32211 500.88891 485.77325 489.26815 476.03207 469.77734 466.56793 493.62396 482.78839 470.33157 462.17074 477.09906 470.76757 489.31381 486.11468 475.64276 471.49072 482.00595 485.38873 480.53643 475.79977 469.22253 488.72970 481.01446 493.13934 486.96911 481.62371 469.96023 488.82580 482.96316 476.70632 487.02590 487.53659 476.29904 472.44818 479.97314 477.46865 473.29275 469.93447 474.75863 472.98861 478.05273 486.17233 480.43383 475.78836 482.39563 480.41461 476.73916 490.22122 482.99255 478.54370 480.67889 478.16925 479.58938 474.47232 484.70156 484.90008 481.15057 - wanted temperatures from the 1st computer: 0.00 326.691895 294.764709 298.554596 282.649414 307.463135 291.600189 300.543671 299.999359 297.054443 305.510986 303.078583 299.970428 299.137207 297.810272 298.365875 298.783813 301.805695 303.370575 300.340332 301.656372 299.389984 300.836243 296.977936 298.827637 299.861847 300.578522 296.483398 296.462646 302.666473 297.978180 304.715515 300.773193 300.172913 307.178711 298.444183 312.749542 302.172089 301.957428 303.820526 303.579712 296.149872 296.983826 303.023834 299.992371 299.144897 295.73 305.296722 304.449219 309.249756 302.303375 304.800293 301.949646 302.895538 307.148254 298.277069 302.761719 296.531281 296.709900 298.417542 300.391022 297.293732 299.136353 290.259125 299.269531 305.229675 301.938751 301.106384 301.689117 295.249969 298.655914 296.441071 300.491364 304.039795 301.149384 295.906250 300.652557 296.303467 300.960083 304.725067 291.927765 303.753845 300.202393 294.915588 297.580017 302.882233 300.872406 306.164551 299.459473 300.940948 306.348328 299.031982 299.465942 297.603119 301.168304 305.233917 292.175751 304.453491 300.391571 303.061188 302.262146 Hope they are the data you wanted. Thanks for your time and help. On Tue, Mar 3, 2015 at 10:30 PM, mah maz mahma...@gmail.com wrote: Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the .gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz mahma...@gmail.com wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote: Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz mahma...@gmail.com wrote: Dear Chaban, Thank you very
Re: [gmx-users] MD on protein-RNA complex
On 3/3/15 8:56 PM, Brett wrote: Dear All, Will you please introduce me a protocol on gromacs molecular dynamics simulation of protein-RNA complex? It's fundamentally no different from any other biomolecule-in-water system. http://www.gromacs.org/Documentation/Tutorials -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.
[gmx-users] MD on protein-RNA complex
Dear All, Will you please introduce me a protocol on gromacs molecular dynamics simulation of protein-RNA complex? Brett -- 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] regarding glycolipids parameters for GROMACS
Dear gromacs users, I was wondering, are they glycolipids (MGDG more specifically) parameters availably for gromacs package? it doesn’t matter for which forcefield they were constructed. Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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] high temperature
On 3/3/15 2:11 AM, mah maz wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? The phrase changed the conditions means nothing to anyone who isn't seeing what you're doing. Post a full .mdp file. -Justin Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote: Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz mahma...@gmail.com wrote: Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production step(around 500k). I have changed the mdp file several times but it doesn't work. What are the possible causes of problem? Thank you! dt = 0.0001 tinit = 0 nsteps = 200 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = cut-off rcoulomb= 0.9 rvdw= 0.9 rvdw_switch = 0.5 vdwtype = switch pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 ref_t = 300 tc_grps = CNT gen_temp= 300 pcoupl = no -- == 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.
Re: [gmx-users] Bond connectivity not found during visualization in VMD
On 3/3/15 2:22 AM, soumadwip ghosh wrote: Hi all, I have made an initial structure for simulating a hybrid of swCNT and ssDNA using Tubegen software for swCNT. The force field I use is CHARMM 27. I have simulated the same DNA in this force field multiple times but for inserting CNT in the system I modified the aminoacids.rtp file according to the bond and atom types mentioned in the PDB I created. I used the aromatic atomtype CA and HP for CNT which is consistent with literature J. Chem. Phys. 136, 175101 (2012). But there is one problem. When I want to visualize the .gro file of the hybrid I can see the bonds between atoms in the DNA while the atoms in the CNT are appearing as only spheres without any bond connection. I am using VMD for visualizing the structures. I feel that there is some error in the [bonds] directive in the aminoacids.rtp file a part of which is shown below. VMD guesses what it thinks the bonds are. What you see is not definitive; the topology is. -Justin [ 1MY0 ] [ atoms ] H1 HP0.141 1 C1 CA -0.111 2 C28 CA -0.011 3 C29 CA -0.010 4 C56 CA -0.003 5 C57 CA -0.001 6 C84 CA -0.002 7 C85 CA -0.002 8 C112 CA -0.001 9 C113 CA -0.001 10 C140 CA -0.002 11 C141 CA -0.002 12 C168 CA -0.001 13 C169 CA -0.003 14 C196 CA -0.010 15 C197 CA -0.011 16 C224 CA -0.111 17 H28 HP0.141 18 C223 CA -0.111 19 H27 HP0.141 20 C222 CA -0.011 21 C221 CA -0.011 22 C220 CA -0.111 23 H26 HP0.141 24 C219 CA -0.111 25 and so on [ bonds ] 12 213 251 324 250 435 213 546 187 657 212 768 186 879 161 98 10 135 109 11 160 11 10 12 134 12 11 13 109 13 12 14 83 14 13 15 108 15 14 16 82 16 15 17 57 17 16 18 19 18 17 19 17 20 21 20 19 21 19 22 82 22 21 23 79 23 22 24 25 24 23 25 23 26 27 26 25 27 25 28 78 28 27 29 75 29 28 30 31 30 29 31 29 32 33 and so on... Am I i observing this in VMD because I put the numbers of atoms instead of atom names ( like C2, H1, C219 etc) in the .rtp file? Also, has the generation of all-atom PDB/ united atom PDB got anything to with it? I made united atom PDB by the way. I really dont know how to avoid this strange observation. Any kind of help will be truly appreciated. Thanks for your time in advance Soumadwip Ghosh Research Fellow, IITB, Mumbai, India -- == 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.
[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems
Dear all, I am going to investigate the interaction between poly(amidoamine) dendrimers with different generations, cores, and surface groups (NH2, COOH, OH, etc) and some low soluble drugs such as curcumines and chalcones. So, I should perform a productive MD run on the dendrimer nanostructures and then dock drug into dendrimer and subsequently I should perform a productive MD on dendrimer-drug complexes. But, I couldn't find an appropriate FF for this purpose. What FF in GROMACS do you think can work for me? Thanks Farideh -- 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.
