Re: [gmx-users] Pressure Coupling in GROMACS
Thanks for your reply Dr. Lemkul. I came across some of the widely fluctuating pressures before but the average pressure was more or less close to the target values previously (even though the instantaneous values varied quite a lot). But in my case, the average pressure is far different from the target values. The pressure curve I am generating using g_energy is attached here. PS. I have 2 carbon nanotubes in my system; one of them is entirely frozen and the other one is entirely free. Is anything wrong with my system? Thanks in advance. On Mon, Jun 8, 2015 at 7:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/8/15 9:10 AM, Jashimuddin Ashraf wrote: Dear GROMACS users, I am new to GROMACS. My system contains only carbon nanotubes and inside my md.mdp file I have- . . Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1; @pressure coupling 1ps compressibility = 4.5e-5; ref_p= 1.0; @reference pressure . . whenever I run the grompp command, I get a warning called- Using Berendsen pressure coupling invalidates the true ensemble for the thermostat I looked up at the mail list where I found Parrinello-Rahman to be appropriate for the NPT simulations. But I intend to run production MD. Is this an error to be worried about? (I can obviously run simulations using maxwarn) Don't confuse common jargon with more strict definitions. Running NPT doesn't mean it's different than production MD. Your data collection can be done with any ensemble that makes sense. NPT is an ensemble. The Berendsen algorithms are generally pretty useful for quickly relaxing temperature/pressure to target values during initial equilibration, but their distributions are (as grompp says) not strictly correct statistical mechanical ensembles. If you want to run under an NPT ensemble, use Parrinello-Rahman for data collection. I have another problem. When I simulated carbon nanotubes with water/ other molecules, the average pressure I observed from simulation (using g_energy command) had a good agreement with the ref_p. But now the average pressure becomes independent of my ref_p. This is a problem that is bugging me for a long time. How can I resolve this? You'll have to provide quantitative evidence of what you're talking about. Pressure fluctuates wildly during a simulation; see extensive previous discussions and notes on the wiki. -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] Simulation of Carbon Nanotubes with bending deformities
Dear gromacs users, I am simulating carbon nanotubes in GROMACS. So far I have only simulated straight CNTs. Now I'd also like to simulate CNTs with bending deformities. I have generated a bent .pdb of my nanotube structure and the simulation runs without any error (I have run the energy minimization and the structure after energy minimization is quite okay). But my problem is as soon as I run the simulation, the bent CNT goes straight within a few pico seconds. Is this because of my forcefield (I have only considered a bond length of 0.1418 nm in my forcefield.itp file)? How can I solve this problem? Thanks in advance. -- 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] Giving an initial velocity to a group of atoms
Thanks again for your reply Dr. Lemkul. I was also expecting a disaster because I gave an unrealistic starting velocity of the structure. But the simulation was running fine. I tried using the gmxdump and found that the velocities I am getting are not the velocities I've given to the atoms. In your reply you were kind to reply that You need to use proper formatting I am following the format in the lilnk - http://chembytes.wikidot.com/g-grofile what I did was I just added 3 extra columns to my .gro file manually after getting .gro file from editconf. What might be my problem? Thanks in advance. On Sun, May 3, 2015 at 10:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/3/15 5:51 AM, Jashimuddin Ashraf wrote: Thanks for your reply Dr. Lemkul. I was simulating a small carbon nanotube to test the idea. So, I added three extra columns after the coordinates inside my .gro file like this- == Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm 64 1CC1 10.539 10.000 10.061 1 0 0 1CC2 10.534 10.070 10.183 1 0 0 1CC3 10.539 10.000 9.817 1 0 0 1CC4 10.498 10.206 9.939 1 0 0 1CC5 10.534 10.070 9.939 1 0 0 1CC6 10.466 10.269 10.061 1 0 0 1CC7 10.498 10.206 10.183 1 0 0 1CC8 10.381 10.381 9.817 3 0 0 1CC9 10.466 10.269 9.817 3 0 0 1CC 10 10.328 10.427 9.939 3 0 0 1CC 11 10.381 10.381 10.061 3 0 0 1CC 12 10.206 10.498 10.183 3 0 0 1CC 13 10.328 10.427 10.183 3 0 0 1CC 14 10.139 10.520 9.817 3 0 0 1CC 15 10.206 10.498 9.939 3 0 0 1CC 16 10.000 10.539 10.061 3 0 0 1CC 17 10.139 10.520 10.061 3 0 0 1CC 18 9.930 10.534 10.183 3 0 0 1CC 19 10.000 10.539 9.817 3 0 0 1CC 20 9.794 10.498 9.939 3 0 0 1CC 21 9.930 10.534 9.939 3 0 0 1CC 22 9.731 10.466 10.061 3 0 0 1CC 23 9.794 10.498 10.183 3 0 0 1CC 24 9.619 10.381 9.817 3 0 0 1CC 25 9.731 10.466 9.817 3 0 0 1CC 26 9.573 10.328 9.939 3 0 0 1CC 27 9.619 10.381 10.061 3 0 0 1CC 28 9.502 10.206 10.183 3 0 0 1CC 29 9.573 10.328 10.183 3 0 0 1CC 30 9.480 10.139 9.817 3 0 0 1CC 31 9.502 10.206 9.939 3 0 0 1CC 32 9.461 10.000 10.061 3 0 0 1CC 33 9.480 10.139 10.061 3 0 0 1CC 34 9.466 9.930 10.183 3 0 0 1CC 35 9.461 10.000 9.817 3 0 0 1CC 36 9.502 9.794 9.939 3 0 0 1CC 37 9.466 9.930 9.939 3 0 0 1CC 38 9.534 9.731 10.061 3 0 0 1CC 39 9.502 9.794 10.183 3 0 0 1CC 40 9.619 9.619 9.817 3 0 0 1CC 41 9.534 9.731 9.817 3 0 0 1CC 42 9.672 9.573 9.939 3 0 0 1CC 43 9.619 9.619 10.061 3 0 0 1CC 44 9.794 9.502 10.183 3 0 0 1CC 45 9.672 9.573 10.183 3 0 0 1CC 46 9.861 9.480 9.817 3 0 0 1CC 47 9.794 9.502 9.939 3 0 0 1CC 48 10.000 9.461 10.061 3 0 0 1CC 49 9.861 9.480 10.061 3 0 0 1CC 50 10.070 9.466 10.183 3 0 0 1CC 51 10.000 9.461 9.817 3 0 0 1CC 52 10.206 9.502 9.939 3 0 0 1CC 53 10.070 9.466 9.939 3 0 0 1CC 54 10.269 9.534 10.061 3 0 0 1CC 55 10.206 9.502 10.183 3 0 0 1CC 56 10.381 9.619 9.817 3 0 0 1CC 57 10.269 9.534 9.817 3 0 0 1CC 58 10.427 9.672 9.939 3 0 0 1CC 59 10.381 9.619 10.061 3 0 0 1CC 60 10.498 9.794 10.183 3 0 0 1CC 61 10.427 9.672 10.183 3 0 0 1CC 62 10.520 9.861 9.817 3 0 0 1CC 63 10.498 9.794 9.939 3 0 0 1CC 64 10.520 9.861 10.061 3 0 0 20.0 20.0 20.0 == You need to use proper formatting; check the .tpr with gmx dump to verify that you're getting what you
Re: [gmx-users] Giving an initial velocity to a group of atoms
Thanks for your reply Dr. Lemkul. I was simulating a small carbon nanotube to test the idea. So, I added three extra columns after the coordinates inside my .gro file like this- == Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm 64 1CC1 10.539 10.000 10.061 1 0 0 1CC2 10.534 10.070 10.183 1 0 0 1CC3 10.539 10.000 9.817 1 0 0 1CC4 10.498 10.206 9.939 1 0 0 1CC5 10.534 10.070 9.939 1 0 0 1CC6 10.466 10.269 10.061 1 0 0 1CC7 10.498 10.206 10.183 1 0 0 1CC8 10.381 10.381 9.817 3 0 0 1CC9 10.466 10.269 9.817 3 0 0 1CC 10 10.328 10.427 9.939 3 0 0 1CC 11 10.381 10.381 10.061 3 0 0 1CC 12 10.206 10.498 10.183 3 0 0 1CC 13 10.328 10.427 10.183 3 0 0 1CC 14 10.139 10.520 9.817 3 0 0 1CC 15 10.206 10.498 9.939 3 0 0 1CC 16 10.000 10.539 10.061 3 0 0 1CC 17 10.139 10.520 10.061 3 0 0 1CC 18 9.930 10.534 10.183 3 0 0 1CC 19 10.000 10.539 9.817 3 0 0 1CC 20 9.794 10.498 9.939 3 0 0 1CC 21 9.930 10.534 9.939 3 0 0 1CC 22 9.731 10.466 10.061 3 0 0 1CC 23 9.794 10.498 10.183 3 0 0 1CC 24 9.619 10.381 9.817 3 0 0 1CC 25 9.731 10.466 9.817 3 0 0 1CC 26 9.573 10.328 9.939 3 0 0 1CC 27 9.619 10.381 10.061 3 0 0 1CC 28 9.502 10.206 10.183 3 0 0 1CC 29 9.573 10.328 10.183 3 0 0 1CC 30 9.480 10.139 9.817 3 0 0 1CC 31 9.502 10.206 9.939 3 0 0 1CC 32 9.461 10.000 10.061 3 0 0 1CC 33 9.480 10.139 10.061 3 0 0 1CC 34 9.466 9.930 10.183 3 0 0 1CC 35 9.461 10.000 9.817 3 0 0 1CC 36 9.502 9.794 9.939 3 0 0 1CC 37 9.466 9.930 9.939 3 0 0 1CC 38 9.534 9.731 10.061 3 0 0 1CC 39 9.502 9.794 10.183 3 0 0 1CC 40 9.619 9.619 9.817 3 0 0 1CC 41 9.534 9.731 9.817 3 0 0 1CC 42 9.672 9.573 9.939 3 0 0 1CC 43 9.619 9.619 10.061 3 0 0 1CC 44 9.794 9.502 10.183 3 0 0 1CC 45 9.672 9.573 10.183 3 0 0 1CC 46 9.861 9.480 9.817 3 0 0 1CC 47 9.794 9.502 9.939 3 0 0 1CC 48 10.000 9.461 10.061 3 0 0 1CC 49 9.861 9.480 10.061 3 0 0 1CC 50 10.070 9.466 10.183 3 0 0 1CC 51 10.000 9.461 9.817 3 0 0 1CC 52 10.206 9.502 9.939 3 0 0 1CC 53 10.070 9.466 9.939 3 0 0 1CC 54 10.269 9.534 10.061 3 0 0 1CC 55 10.206 9.502 10.183 3 0 0 1CC 56 10.381 9.619 9.817 3 0 0 1CC 57 10.269 9.534 9.817 3 0 0 1CC 58 10.427 9.672 9.939 3 0 0 1CC 59 10.381 9.619 10.061 3 0 0 1CC 60 10.498 9.794 10.183 3 0 0 1CC 61 10.427 9.672 10.183 3 0 0 1CC 62 10.520 9.861 9.817 3 0 0 1CC 63 10.498 9.794 9.939 3 0 0 1CC 64 10.520 9.861 10.061 3 0 0 20.0 20.0 20.0 == but my simulation does not seem to have any effect of this. I tried increasing the value but it did not change the results. How can I solve this? Thanks in advance. On Sat, May 2, 2015 at 10:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/15 12:27 PM, Jashimuddin Ashraf wrote: Dear Gromacs users, I was wondering if it is possible to give an initial velocity to any group of atoms in GROMACS? I went through the manual but could not find any suitable solution to it. Is the parameters related to Velocity generation in the .mdp file somehow related to this? No, those options are only for specifying whether or not random velocities should be generated. Velocities are read from .trr, .cpt, or .gro files. Writing the desired velocities in the .gro is likely the easiest approach. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical
Re: [gmx-users] Gromacs on Nvidia 830M
I run GROMACS in my AMD core 2 duo laptop with 4GB memory. I have been using it for more than a year. No problem whatsoever. On Mon, Apr 6, 2015 at 2:51 PM, Александр Селютин saga1...@gmail.com wrote: 2015-04-06 12:57 GMT+06:00 B P 4grom...@gmail.com: ... Has anyone tried? I use gmx on laptop(i5 3210, nvidia 620m) but for using cuda additional cooling is needed. -- Regards, Alexander Selyutin -- 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] Gromacs on Nvidia 830M
May be the longest simulation that I did was 1ns with a dt = 0.002. I forgot how long it took. Usually I do not run my laptop over 10 hours a day, So, quite possibly it took me a lot of days (I had roughly 2 atoms in my system) On Tue, Apr 7, 2015 at 12:20 PM, B P 4grom...@gmail.com wrote: How long were your simulations? How many nanoseconds/day? what were your dt values? Sorry for so many queries at once.. but your reply made me curious.. Radeon R5 btw? Or NVIDIA? If NVIDIA, did you try with CUDA? On Tue, Apr 7, 2015 at 11:39 AM, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com wrote: I run GROMACS in my AMD core 2 duo laptop with 4GB memory. I have been using it for more than a year. No problem whatsoever. On Mon, Apr 6, 2015 at 2:51 PM, Александр Селютин saga1...@gmail.com wrote: 2015-04-06 12:57 GMT+06:00 B P 4grom...@gmail.com: ... Has anyone tried? I use gmx on laptop(i5 3210, nvidia 620m) but for using cuda additional cooling is needed. -- Regards, Alexander Selyutin -- 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. -- 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 liquid SO2 (Sulphur dioxide)
Dear gromacs users, I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create an equilibrated structure of SO2 molecules using the gmx insert-molecules function. As I try to minimize the energy of the system, I always get this- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 10 (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. I tried to analyze my .gro file that the gmx insert-molecules function is returning me and found that some of my SO2 have a bond in between them. Is this what causes the energy minimization to crash? Is there any way I can prepare an equilibrated system of liquid SO2 ? My SO2.itp file is like this (I made this an .itp because I wish to study this system along with some other molecules)- [ moleculetype ] ; Name nrexcl SO23 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_202 1 SR S 1 0.6512 32.07 ;qtot 0.6512 2 opls_326 1 SR O1 2-0.3256 15.99940 ;qtot 0.3256 3 opls_326 1 SR O2 3-0.3256 15.99940 ; qtot 0 ; opls_202 S 16 32.07 0.6512 A3.61500e-01 1.2125232 ; opls_326 O 8 15.99940-0.3256 A3.00500e-01 0.47756176 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 0.1434 635968.0 1 3 1 0.1434635968.0 [ distance_restraints ] ; aiaj type index type' low up1 up2 fac 1 2 1 0 1 1.149 1.490 1.490 1.0 1 3 1 0 1 1.149 1.490 1.490 1.0 [ angles ] ; aiajak functc0c1 c2c3 2 1 3 1119.51359.8 I have also uploaded the .gro file that the gmx insert-molecules function is returning me after this text. SO2_box300.gro https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web Thanks in advance. -- 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] Simulation of polarizable Carbon nanotubes
Thanks again for your reply Dr. Lemkul. I was wondering about the update regarding publishing the codes. Are the codes ready to be published? Actually I could not get my work done and it seems I have to wait until the codes/ patch are available. Thanks in advance. On Wed, Mar 4, 2015 at 10:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/15 11:07 AM, Peter Kroon wrote: On 03/04/2015 04:48 PM, Jashimuddin Ashraf wrote: Thanks for your reply Dr.Peter Kroon and Dr. Lemkul. The virtual_sitesn Im not a Dr. yet ;) directive is very helpful in declaring the virtual site positions. Now, the simulation runs fine in vacuum. But as soon as I solvate the system in water, the production MD fails with- . . . MDStep= 91/ 9 EPot: -6.87315918e+02, rmsF: 1.75e+03 MDStep= 91/10 EPot: -7.87661133e+02, rmsF: 1.44e+03 MDStep= 91/11 EPot: -8.65109253e+02, rmsF: 1.22e+03 MDStep= 91/12 EPot: -9.25257446e+02, rmsF: 1.06e+03 MDStep= 91/13 EPot: -9.72217041e+02, rmsF: 9.53e+02 MDStep= 91/14 EPot: -1.00904297e+03, rmsF: 8.72e+02 MDStep= 91/15 EPot: -1.03802905e+03, rmsF: 8.10e+02 MDStep= 91/16 EPot: -1.06091382e+03, rmsF: 7.61e+02 MDStep= 91/17 EPot: -1.07902722e+03, rmsF: 7.23e+02 MDStep= 91/18 EPot: -1.09339343e+03, rmsF: 6.93e+02 MDStep= 91/19 EPot: -1.10480664e+03, rmsF: 6.70e+02 step 91: EM did not converge in 20 iterations, RMS force 579.612 MDStep= 92/ 0 EPot: -1.14934949e+03, rmsF: 7.17e+02 Segmentation fault (core dumped) I found that at lower value of the polarizability (alpha_zz), the simulation goes fine (in water). The simulation also goes well if I decrease the charges of the carbon atoms and the shell. But at the values of alpha (0.1296 nm^3) and charges of the carbon atoms (0.25e) as the paper mentioned, the simulation ends with this error. In your message, you were kind to reply with- If your simulation blows up, try analysing the distance between the shell and it's parent; it should give you a hint about what's going wrong. In my case, the distance between the shell and it's parent goes higher with the increase of the value of alpha. But I cannot understand what is causing the system to blow up. It would be very much helpful if you could help me with this error. See Justin's answer for an explanation. As for blowing up: if the shell particle moves from it's parent far enough to reach a positively charged particle the attraction will become VERY large, blowing up your system. Check your exclusion list with the original paper. It could be you need to exclude more. For example: CHARMM treats drude/shell particles in such a way that if two atoms are in a 1-4 relationship, their drude/shell particles are as well. According to GROMACS, these would have a 1-6 relationship. ...all of which are normal nonbonded relationships. Note that our Drude force field does Thole screening for 1-2 and 1-3 interactions (based on the parent atoms, not the Drudes, which in a 1-3 interaction of parent atoms would actually be 1-5 interaction for Drudes without this special classification), but anything beyond that is just normal. -Justin Good luck! Peter Kroon thanks in advance. On Mon, Feb 23, 2015 at 6:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/23/15 3:47 AM, Peter Kroon wrote: On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote: Thanks for your reply Dr. Lemkul I changed the bond length to zero in my topology file, forcefield file and in the n2t file. I also added the [ exclusion] section- If memory serves, you don't need a bond between a shell particle and it's parent; the polarization directive takes care of it's position. If you want, you can define a non-interacting connection (bond type 5) between them. This is correct. The [polarization] directive is just another bonded interaction. The value of the force constant is back-calculated from the atomic polarizability, alpha. [ exclusions ] ; iatom excluded from interaction with i 123456 7 8 213456 7 8 312456 7 8 412356 7 8 512346 7 8 61234578 7123456 8123456 in my topology. But the same error keeps showing up. What did I possibly do wrong? AFAIK this will exclude all atoms from eachother. Just the last line should be enough if you just want to exclude the shell-carbon interactions In your mail, you were kind to reply with- I only looked at the paper briefly, but it seems they are working with a model that makes use
[gmx-users] ethanol solvation (equilibrated ethanol .gro file)
Dear Gromacs users, I want to create an ethanol solution to study CNT in ethanol dynamics. How can I get/generate an equilibrated ethanol .gro file (like the methanol216.gro or spc216.gro files)? I tried to use the genbox function but the cannot get the density of the solution right. Just to test my files, I ran a simulation of a box containing about 600 ethanols. At the production MD, I came across this warning- The bond in molecule-type Ethanol between atoms 4 OH and 5 HH has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. The warning vanished as I reduced my time step by half. But inside my md.mdp file I still had no constraints- OPTIONS FOR BONDS constraints = none constraint-algorithm = shake Am I doing anything wrong here? Any comment/suggestion would be very much helpful for me. Thanks in advance. -- 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] Simulation of polarizable Carbon nanotubes
Thanks for your reply Dr.Peter Kroon and Dr. Lemkul. The virtual_sitesn directive is very helpful in declaring the virtual site positions. Now, the simulation runs fine in vacuum. But as soon as I solvate the system in water, the production MD fails with- . . . MDStep= 91/ 9 EPot: -6.87315918e+02, rmsF: 1.75e+03 MDStep= 91/10 EPot: -7.87661133e+02, rmsF: 1.44e+03 MDStep= 91/11 EPot: -8.65109253e+02, rmsF: 1.22e+03 MDStep= 91/12 EPot: -9.25257446e+02, rmsF: 1.06e+03 MDStep= 91/13 EPot: -9.72217041e+02, rmsF: 9.53e+02 MDStep= 91/14 EPot: -1.00904297e+03, rmsF: 8.72e+02 MDStep= 91/15 EPot: -1.03802905e+03, rmsF: 8.10e+02 MDStep= 91/16 EPot: -1.06091382e+03, rmsF: 7.61e+02 MDStep= 91/17 EPot: -1.07902722e+03, rmsF: 7.23e+02 MDStep= 91/18 EPot: -1.09339343e+03, rmsF: 6.93e+02 MDStep= 91/19 EPot: -1.10480664e+03, rmsF: 6.70e+02 step 91: EM did not converge in 20 iterations, RMS force 579.612 MDStep= 92/ 0 EPot: -1.14934949e+03, rmsF: 7.17e+02 Segmentation fault (core dumped) I found that at lower value of the polarizability (alpha_zz), the simulation goes fine (in water). The simulation also goes well if I decrease the charges of the carbon atoms and the shell. But at the values of alpha (0.1296 nm^3) and charges of the carbon atoms (0.25e) as the paper mentioned, the simulation ends with this error. In your message, you were kind to reply with- If your simulation blows up, try analysing the distance between the shell and it's parent; it should give you a hint about what's going wrong. In my case, the distance between the shell and it's parent goes higher with the increase of the value of alpha. But I cannot understand what is causing the system to blow up. It would be very much helpful if you could help me with this error. thanks in advance. On Mon, Feb 23, 2015 at 6:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/23/15 3:47 AM, Peter Kroon wrote: On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote: Thanks for your reply Dr. Lemkul I changed the bond length to zero in my topology file, forcefield file and in the n2t file. I also added the [ exclusion] section- If memory serves, you don't need a bond between a shell particle and it's parent; the polarization directive takes care of it's position. If you want, you can define a non-interacting connection (bond type 5) between them. This is correct. The [polarization] directive is just another bonded interaction. The value of the force constant is back-calculated from the atomic polarizability, alpha. [ exclusions ] ; iatom excluded from interaction with i 123456 7 8 213456 7 8 312456 7 8 412356 7 8 512346 7 8 61234578 7123456 8123456 in my topology. But the same error keeps showing up. What did I possibly do wrong? AFAIK this will exclude all atoms from eachother. Just the last line should be enough if you just want to exclude the shell-carbon interactions In your mail, you were kind to reply with- I only looked at the paper briefly, but it seems they are working with a model that makes use of anisotropic polarization. In GROMACS, this is currently only available for water, so the model would not be supported. Are you suggesting that, this model is something we should not work with in GROMACS right now? (I am really sorry, I could not understand this part properly) From my quick read of the paper (focusing only a narrow section of the methods), the authors list alpha_zz only, implying that the shell is only polarizable along the normal to the ring. Therefore the other elements of the polarization tensor are zero. Also, it would be very nice, if you could give us an idea about the time required to publish the codes and adding them in the new versions of GROMACS. That depends on reviewers :) The paper should be submitted this week, after which I will be working to submit the code to the master development branch. The code will not be included in 5.1 (I missed the deadline, due to some debugging that took longer than expected), but the code will be available as a patch to the master branch in the coming weeks. -Justin Thanks in advance, Lastly, for defining the virtual site you could look at the virtual_sitesn directives and define a center of geometry or a center of mass. Im not sure if it has any advantages over a virtual site as it is defined now though. If your simulation blows up, try analysing the distance between the shell and it's parent; it should give
Re: [gmx-users] Simulation of polarizable Carbon nanotubes
Thanks for your reply Dr. Lemkul I changed the bond length to zero in my topology file, forcefield file and in the n2t file. I also added the [ exclusion] section- [ exclusions ] ; iatom excluded from interaction with i 123456 7 8 213456 7 8 312456 7 8 412356 7 8 512346 7 8 61234578 7123456 8123456 in my topology. But the same error keeps showing up. What did I possibly do wrong? In your mail, you were kind to reply with- I only looked at the paper briefly, but it seems they are working with a model that makes use of anisotropic polarization. In GROMACS, this is currently only available for water, so the model would not be supported. Are you suggesting that, this model is something we should not work with in GROMACS right now? (I am really sorry, I could not understand this part properly) Also, it would be very nice, if you could give us an idea about the time required to publish the codes and adding them in the new versions of GROMACS. Thanks in advance, On Sat, Feb 21, 2015 at 12:20 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/20/15 12:57 PM, Jashimuddin Ashraf wrote: Dear users, I want to perform a molecular dynamic simulation of polarizable carbon nanotubes. I intend to implement this paper- http://www.sciencedirect.com/science/article/pii/S0927025607000456 I digged up the manual but could not find much help from it. I went through some mails in the gromacs user maillist, studied some .itp files and learned some elementary stuffs regarding the addition of virtual sites and shell atoms.I understand that I have to add both shell and virtual sites in this case. Now, before jumping right into a big nanotube molecule, I was trying to perform a simulation with a single benzene ring with a virtual site placed at the center and a shell attached to the virtual site. In my forcefield.itp file have the virtual site and the shell declared like this- - [ atomtypes ] ; name mass chargeptype sigma eps CJ1 1 12.01100 0.25 A 3.4e-01 3.60100e-01 VS1 00 D 0 0 SL 1 0 -1.5 S 00 [ bondtypes ] `; ij func b0 kbgamma CJ1CJ1 30.1418 478.900021.867 VS SL 10.06 2409 - Here, I have considered a bond between the virtual site and the shell (the paper mentions something like it but does not provide with the bond length). Is it a mistake? The equilibrium bond length should be zero (i.e. no induced polarization). and inside my topol.top file, I have- - [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1CJ1 1 C C 10.25 12.011 ; qtot 0.25 2CJ1 1 C C 10.25 12.011 ; qtot 0.5 3CJ1 1 C C 10.25 12.011 ; qtot 0.75 4CJ1 1 C C 10.25 12.011 ; qtot 1.00 5CJ1 1 C C 10.25 12.011 ; qtot 1.25 6CJ1 1 C C 10.25 12.011 ; qtot 1.50 7 VS 1 C VS 10 0 ; qtot 1.50 8 SL 1 C S 1 -1.5 0; qtot 0 [ polarization ] ; virtual_siteshellfunctiontypealpha (in nm^3) 7810.1 I only looked at the paper briefly, but it seems they are working with a model that makes use of anisotropic polarization. In GROMACS, this is currently only available for water, so the model would not be supported. It will be soon (I know I've been saying that for a while, but our paper regarding Drude simulations in GROMACS is just about done, after which I can provide the code). [ bonds ] ; aiaj functc0c1c2c3 1 2 3 1 5 3 2 4 3 3 4 3 3 6 3 5 6 3 7 8 1 [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 5 1 2 4 3 2 1 5 6 3 1 2 4 3 3
[gmx-users] Simulation of polarizable Carbon nanotubes
Dear users,
I want to perform a molecular dynamic simulation of polarizable carbon
nanotubes. I intend to implement this paper-
http://www.sciencedirect.com/science/article/pii/S0927025607000456
I digged up the manual but could not find much help from it. I went through
some mails in the gromacs user maillist, studied some .itp files and
learned some elementary stuffs regarding the addition of virtual sites and
shell atoms.I understand that I have to add both shell and virtual sites in
this case.
Now, before jumping right into a big nanotube molecule, I was trying to
perform a simulation with a single benzene ring with a virtual site placed
at the center and a shell attached to the virtual site.
In my forcefield.itp file have the virtual site and the shell declared like
this-
-
[ atomtypes ]
; name mass chargeptype sigma eps
CJ1 1 12.01100 0.25 A 3.4e-01 3.60100e-01
VS1 00 D 0 0
SL 1 0 -1.5 S 00
[ bondtypes ]
`; ij func b0 kbgamma
CJ1CJ1 30.1418 478.900021.867
VS SL 10.06 2409
-
Here, I have considered a bond between the virtual site and the shell (the
paper mentions something like it but does not provide with the bond
length). Is it a mistake?
and inside my topol.top file, I have-
-
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeBchargeB massB
1CJ1 1 C C 10.25 12.011 ;
qtot 0.25
2CJ1 1 C C 10.25 12.011 ;
qtot 0.5
3CJ1 1 C C 10.25 12.011 ;
qtot 0.75
4CJ1 1 C C 10.25 12.011 ;
qtot 1.00
5CJ1 1 C C 10.25 12.011 ;
qtot 1.25
6CJ1 1 C C 10.25 12.011 ;
qtot 1.50
7 VS 1 C VS 10 0 ;
qtot 1.50
8 SL 1 C S 1 -1.5 0;
qtot 0
[ polarization ]
; virtual_siteshellfunctiontypealpha (in nm^3)
7810.1
[ bonds ]
; aiaj functc0c1c2c3
1 2 3
1 5 3
2 4 3
3 4 3
3 6 3
5 6 3
7 8 1
[ dihedrals ]
; aiajakal functc0c1
c2c3c4c5
5 1 2 4 3
2 1 5 6 3
1 2 4 3 3
6 3 4 2 3
4 3 6 5 3
1 5 6 3 3
[ virtual_sites3 ]
; detailed calculation not shown here
; Dummy fromfunctab
7 4 5 61 0.50
-
I ran an energy minimization for an emtol of 100 but it gives me a result
like this-
Steepest Descents converged to machine precision in 141 steps,
but did not reach the requested Fmax 100.
Potential Energy = -6.1810545e+06
Maximum force = 9.1656689e+12 on atom 4
Norm of force = 4.5828344e+12
-
If I run a production MD with this, the simulation blows up with this-
MDStep= 40/18 EPot: nan, rmsF:nan
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
MDStep= 40/19 EPot: nan, rmsF:nan
step 40: EM did not converge in 20 iterations, RMS force nan
-
Is something wrong with my system itself? or is there anything wrong with
my methods?
I have been stuck at this for a very long time now and anything- any
comment or hint would be very much helpful for me.
Thanks in advance,
Jashimuddin Ashraf
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[gmx-users] Conversion of Harmonic potential parameters to Morse potential parameters
Dear gromacs users, I have a system containing carbon nanotubes. I have successfullly simulated the system in vacuum. Now i would like to terminate the dangling bonds of the nanotube with Hydrogen atoms. So, I need to modify my forcefield. In the [ bondtypes ] section inside my forcefield.itp I had ; [ bondtypes ] CJCJ 30.1418 478.9000 21.867 ; Now I need to add the bond parameters for carbon-Hydrogen. But unfortunately I have my parameters in Harmonic potential; instead of Morse potential. How can I convert my Harmonic potential parameters to Morse potential parameters? Is there any formula for this? Thanks in advance -- 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.
