Re: [gmx-users] Enthalpy of Vaporization
On Mon, Oct 5, 2015 at 7:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/15 2:01 PM, Rasoul Nasiri wrote: > >> On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 10/5/15 1:50 PM, Pallavi Banerjee wrote: >>> >>> Correct me if I am wrong, please. Ugas would be obtained from a >>>> simulation >>>> of a single molecule in vacuum. And U liq would be the total potential >>>> energy of the system (which is given by g_energy) minus the total bonded >>>> potential energy (bonds+angles+dihedrals). Am I thinking right? >>>> >>>> >>>> No. It's the actual potential energy. You need the whole potential >>> energy to account for flexibility in the molecule. >>> >>> >>> Hopefully FFs can do this because of the anharmonicity effects caused by >> multi-structural effects (e.g., many coupling of torsions). This >> scenario will be serious when T goes up. >> >> > Indeed it depends to some extent on the size, flexibility, and chemical > composition of the molecule. Additive FFs will inherently overestimate > dipole moments to account for a lack of polarization response, so generally > very polar molecules have poor DHvap values with additive models. Simple > hydrophobics are easier and often agree better with experimental data. > It's even complex behaviour for long chain apolar molecules as there are many possibility for taken into account the coupling effects (rot, vib, conf and so on) especially at high T. Rasoul > -- > 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] Enthalpy of Vaporization
This non-zero value becomes quite significant if you are dealing with highly flexible molecules - Internal molecular dynamics effects are different in the gas and liquid phases. Rasoul On Mon, Oct 5, 2015 at 3:53 PM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello Users, > > I need to calculate the cohesive energy for my system, for which the > enthalpy of vaporization is needed. Am I right to assume that just the > non-bonded interaction energy (potential energy) is required to calculate > the enthalpy of vaporization ? > > Many Thanks! > > -Pallavi Banerjee > -- > 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] the growth of the molecule
On Mon, Sep 22, 2014 at 7:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/22/14 10:45 AM, Александр Селютин wrote: Thanks to everyone I have idea that I can stop simulation, change topology(move end of molecule, add new atoms) and start again. It should be repeated every 2 ps. But it can be very slowly. Does anybody know how to do it more correctly? I don't know that there is a good solution. What you've outlined also doesn't seem very reliable, because you're causing serious perturbations to the system every 2 ps, so the outcome of the previous simulation is basically lost because you have changed the coordinates and perturbed the solvent around the polymer. So you basically have a certain number of unequilibrated polymer systems of varying size. It doesn't help you to determine much of anything. MD is great for simulating nonbonded aggregation/assembly, but it is not trivial to do something involving covalent bonds in classical MD. If you want to study dynamic of growth of materials via formation of chemical bonds (covalent, ionic and even metallic), perhaps empirical reactive FFs might be acceptable choices in terms of cost and accuracy BUT those are not implemented in GROMACS as far as I know. You need try them using LAMMPS, ADF, ReaxFF codes,. Rasoul 2014-09-18 20:03 GMT+07:00 Tamas Karpati tkarp...@gmail.com: Dear Alexander, As Vitaly has already suggested, it is possible to simulate growth. I'd, on the other hand, underline what Micholas has said. It may take some planning. Here are a few ideas how to do it. 1. If you are simulating cleaving/forming bonds, the topology would change which is difficult for normal MD runs. If, however, running just few steps (or probably a single step) MD job and analysing/regenerating the topology after each such step (by your specific scripts) you may be fine. It can take some coding. 2. You can still go on by replacing explicite bonds by Morse or LJ potentials (or using any tabled ones). Although such model can be poor in describing the underlying chemistry a good fitting of Morse/LJ/etc. can give you an acceptable rate for the polymerisation. This way bonds could be described by formally non-bonding interactions and the whole system is modelled as an interacting set of individual single atom ions. A complete replacement of all the bonds by non-bonding interaction potentials will give you a bond-less and angle-less etc. TOP file. It can be done in parts, too, in which case just some kinds of bonds (those that cleave or form) would be replaced. It may take lots of preparation but I think its viable. 3. Sorry, I know nothing about special force fields created for sims of reactions. Probably those would be your tools. HTH, toma On Thu, Sep 18, 2014 at 2:10 PM, Smith, Micholas D. smit...@ornl.gov wrote: I should clarify, If you are not concerned with the formation of covalent bonds, you can simulate growth, to some extent. Protein aggregation, for instance, can be studied with MD because of this; so if you are only interested in the early assembly, and not with electronic structure/covalent bonding, than you are ok. I had interpreted your question to be related to bonding, not just early assembly/aggregation. As far as adding units at a given time, I don't think gromacs can do that, as it would require your topology to change while the simulation was running (i.e. adding more molecules to your system while it is running). Now you could run multiple simulations of the polyethylene chain at different lengths with a single unit free in solution, and watch how the chain increases, but I don't think you could run a single simulation where you added monomer units on the fly. -Micholas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dr. Vitaly Chaban vvcha...@gmail.com Sent: Thursday, September 18, 2014 2:43 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] the growth of the molecule Why not? Your interaction potential is responsible for everything. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин saga1...@gmail.com wrote: Can the gromacs simulate the growth of the molecule? For example, does it allow to add units to the polymer chain at certain times? More specifically, it is the increase the chain length of the polyethylene. Thanks! -- 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
Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools
On Mon, Jul 14, 2014 at 12:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/13/14, 8:41 PM, Rasoul Nasiri wrote: On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/13/14, 7:11 PM, Rasoul Nasiri wrote: On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Note that two constrained atoms correspond to one constraint. C12H26 26 constrained atoms due to hydrogens which have been connected to carbon atoms. Number of molecules 2550 therefore 66300 will be total constrained atoms in cell. Note that grompp makes your life easy by printing out the corrected number of degrees of freedom. It should be 3N - 0.5*N_constraints. Based on grompp_d: Number of degrees of freedom in T-Coupling group System is 196338.00 3N-0.5*N_constrants = 196338 N= 96900 ===. N_constraints =188706 T(corrected) = T(g_traj)*N_atoms/(N_atoms-N_constraints) T(g_traj) = 269 K N_atoms = 96900 == T(corrected) = -262 which is unphysical value. any other suggestions/solutions? Note that the desired temperature is 400 K. You're doing the calculation wrong. Number of degrees of freedom that g_traj assumes: 96900 * 3 = 290700 I think translational modes should be reduced, having said this for N total atoms with fixed mumentum into the cell (290700-3) must be more accurate. g_traj has no knowledge of COM treatment, periodicity, etc, so such an operation is not necessary (not that it makes any difference in this case). It hasn't but we know that the conservation of momentum among the cells definitely affect the produced trajectory. I agree it cannot make significant effects in my system but it's not the general case. If anything, the degrees of freedom associated with translational and/or rotational motion have been corrected by grompp, so the manipulation would lie in the denominator, but if using the quantity printed by grompp, you don't need any further subtraction. Having said this if you compare T in two different systems (using PBC and another VBC) obtained by g_traj, you will see there are some differences. -Justin Rasoul -- == 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] inconsistency in obtained temperature values by traj and g_energy tools
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Note that two constrained atoms correspond to one constraint. C12H26 26 constrained atoms due to hydrogens which have been connected to carbon atoms. Number of molecules 2550 therefore 66300 will be total constrained atoms in cell. Note that grompp makes your life easy by printing out the corrected number of degrees of freedom. It should be 3N - 0.5*N_constraints. Based on grompp_d: Number of degrees of freedom in T-Coupling group System is 196338.00 3N-0.5*N_constrants = 196338 N= 96900 ===. N_constraints =188706 T(corrected) = T(g_traj)*N_atoms/(N_atoms-N_constraints) T(g_traj) = 269 K N_atoms = 96900 == T(corrected) = -262 which is unphysical value. any other suggestions/solutions? Note that the desired temperature is 400 K. -Justin Rasoul -- == 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] inconsistency in obtained temperature values by traj and g_energy tools
On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/13/14, 7:11 PM, Rasoul Nasiri wrote: On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Note that two constrained atoms correspond to one constraint. C12H26 26 constrained atoms due to hydrogens which have been connected to carbon atoms. Number of molecules 2550 therefore 66300 will be total constrained atoms in cell. Note that grompp makes your life easy by printing out the corrected number of degrees of freedom. It should be 3N - 0.5*N_constraints. Based on grompp_d: Number of degrees of freedom in T-Coupling group System is 196338.00 3N-0.5*N_constrants = 196338 N= 96900 ===. N_constraints =188706 T(corrected) = T(g_traj)*N_atoms/(N_atoms-N_constraints) T(g_traj) = 269 K N_atoms = 96900 == T(corrected) = -262 which is unphysical value. any other suggestions/solutions? Note that the desired temperature is 400 K. You're doing the calculation wrong. Number of degrees of freedom that g_traj assumes: 96900 * 3 = 290700 I think translational modes should be reduced, having said this for N total atoms with fixed mumentum into the cell (290700-3) must be more accurate. Number of actual degrees of freedom from grompp: 196338 Temperature conversion factor = 290700/196388 = 1.481 It makes sense. Actual T = 269 * 1.481 Actual T = 398.3 K Thanks. -Justin Rasoul -- == 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] inconsistency in obtained temperature values by traj and g_energy tools
On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Please just tell me how values of obtained T by g_traj can be corrected when I use trajectory and tpr files of constrain MD simulations (OPLS) as an input? T(corrected) = T(g_traj)*natoms/(natoms-nconstraints) T(g_traj) 0 269.581 1 271.064 2 271.309 3 271.205 4 271.499 5 270.868 6 272.247 7 271.59 8 271.614 9 270.598 10 271.662 Corrected T based on the abovementione formula: number of atoms : 96900 number of constarined atoms = 66300 Corrected T 853.6732 858.3693 859.1452 858.8158 859.7468 857.7487 862.1155 860.035 860.111 856.8937 860.263 The desired temperature was 400K. Cheers, Tsjerk Rasoul -- 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] inconsistency in obtained temperature values by traj and g_energy tools
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Note that two constrained atoms correspond to one constraint. C12H26 26 constrained atoms due to hydrogens which have been connected to carbon atoms. Number of molecules 2550 therefore 66300 will be total constrained atoms in cell. Cheers, T. Rasoul On Jul 12, 2014 12:01 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Please just tell me how values of obtained T by g_traj can be corrected when I use trajectory and tpr files of constrain MD simulations (OPLS) as an input? T(corrected) = T(g_traj)*natoms/(natoms-nconstraints) T(g_traj) 0 269.581 1 271.064 2 271.309 3 271.205 4 271.499 5 270.868 6 272.247 7 271.59 8 271.614 9 270.598 10 271.662 Corrected T based on the abovementione formula: number of atoms : 96900 number of constarined atoms = 66300 Corrected T 853.6732 858.3693 859.1452 858.8158 859.7468 857.7487 862.1155 860.035 860.111 856.8937 860.263 The desired temperature was 400K. Cheers, Tsjerk Rasoul -- 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.
Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools
On Fri, Jul 11, 2014 at 10:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 9:30 PM, Rasoul Nasiri wrote: On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy? No, not unless they are assigned as separate tc-grps in the .mdp file, as sub-systems are changing during the simulation in terms of number of atoms in a non-equilibrium situation, I don't think g_energy can give relevant temperature values, even tc-grps are specified in mdp. Isn't? No, you can't then. This also makes any sort of interpretation non-trivial; if an atom dissociates from one group to which it was linked, the interpretation of its new velocity when bonding to another group is now somewhat discontinuous, is it not? So it could make clrea why I did not select g_energy for determination of T and replied your question! but then (1) you shouldn't be designing something affecting the physics purely based on what you hope to analyze and (2) you then already know the outcome. This is actually what g_traj can do; like I said, you just have to account for restraints. can you clarify how it can be practically done? You need to recalculate the number of degrees of freedom based on whatever constraints there might be. You said there are none, so that may not be the case. Please excuse the typo in the earlier message, restraints should be constraints. Which DOFs, do I need consider translational and rotational as well as vibrational ones? And how this number will affact crude values obtained by g_traj? Please consider constrained MD simulation done using OPLS. 2- My trajectory is not constrain one as it has been recorded using reactive FF. I need to estimate T with converted trajectory (reaxffgro). Converted trajectory? yes, since non-reactive FF at high temperatures cannot be reliable due to vibrational effects, all my MD has been done by reactive one. Your first post suggested the run was done with Gromacs (being that you had .tpr and .edr files). I have produced .tpr file but not .edr. The outcomes you posted agree perfectly with constrained molecules, The posted data refereed to un-reliability of g_traj for obtaining of T. I just wanted to know the reason via comparison with g_energy. Those obtained by non-reactive FF of OPLS. This is where I was getting confused. Your very first message said you had the same trajectory and input files but clearly this is not true. You're comparing apples and oranges; an accurate statement of what's really going on is very important and saves everyone time. That means all posted values in my first message obtained by ONLY OPLS FF just to understand how much g_traj and g_energy give us different T values on same trajectory and input file. but without more details on what you're actually doing, I'm not going to hazard a guess. Recall that even if you set constraints = none, SETTLE is still applied to water molecules unless you use -DFLEXIBLE (which you shouldn't for most normal purposes). My molecules are not water and g_traj gave following T values for same system using two different FFs 1- ReaxFF 0 399.321 1 400.25 2 401.08 3 401.271 4 400.67 5 400.264 6 400.752 7 401.178 8 401.391 9 399.065 10 401.78 As i said already I just converted reaxff trajectory to gro one and also used tpr file (constrain=none in mdp) for estimation of T with g_traj. 2- OPLS 0 269.581 1 271.064 2 271.309 3 271.205 4 271.499 5 270.868 6 272.247 7 271.59 8 271.614 9 270.598 10 271.662 How constrained MD results (OPLS) can be corrected? Now you're losing me again. You're talking about converting some ReaxFF trajectory without constraints, but were there constraints in the OPLS trajectory? here there are two different values of T obtained by ReaxFF and OPLS. As you told there are no constrains in ReaxFF trajectory BUT there should be constrain in OPLS trajectory. Can you give an actual listing of commands and .mdp files (if applicable) for what you're doing? This is all very confusing. Please just tell me how values of obtained T by g_traj can be corrected when I use trajectory and tpr files of constrain MD simulations (OPLS) as an input? command: g_traj_d -f md.trr -s topol -n n.ndx -ot T.xvg mdp file: ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ;20ns ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated
[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools
Hi, Can anybody tell me why these two tools give different temperature values based on same trajectory and input files? 1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg 0.00 508.066786 1.00 496.066137 2.00 501.665712 3.00 498.809896 4.00 499.838636 5.00 498.828986 6.00 500.653778 2- g_traj -f md_shor.trr -s topol_shor.tpr -ot T-.xvg 0 338.107 1 334.99 2 338.707 3 336.785 4 337.642 5 337.062 6 338.132 the desired temperature was 500 K in mdp file. Thanks, Rasoul -- 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] inconsistency in obtained temperature values by traj and g_energy tools
Is there any other (not g_energy) tools in GROMACS to estimate T properly? Rasoul On Thu, Jul 10, 2014 at 5:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 12:49 PM, Rasoul Nasiri wrote: Hi, Can anybody tell me why these two tools give different temperature values based on same trajectory and input files? 1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg 0.00 508.066786 1.00 496.066137 2.00 501.665712 3.00 498.809896 4.00 499.838636 5.00 498.828986 6.00 500.653778 2- g_traj -f md_shor.trr -s topol_shor.tpr -ot T-.xvg 0 338.107 1 334.99 2 338.707 3 336.785 4 337.642 5 337.062 6 338.132 the desired temperature was 500 K in mdp file. As stated in the help description, g_traj does not correct for constrained degrees of freedom. -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] inconsistency in obtained temperature values by traj and g_energy tools
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy? No, not unless they are assigned as separate tc-grps in the .mdp file, as sub-systems are changing during the simulation in terms of number of atoms in a non-equilibrium situation, I don't think g_energy can give relevant temperature values, even tc-grps are specified in mdp. Isn't? but then (1) you shouldn't be designing something affecting the physics purely based on what you hope to analyze and (2) you then already know the outcome. This is actually what g_traj can do; like I said, you just have to account for restraints. can you clarify how it can be practically done? 2- My trajectory is not constrain one as it has been recorded using reactive FF. I need to estimate T with converted trajectory (reaxffgro). Converted trajectory? yes, since non-reactive FF at high temperatures cannot be reliable due to vibrational effects, all my MD has been done by reactive one. Your first post suggested the run was done with Gromacs (being that you had .tpr and .edr files). I have produced .tpr file but not .edr. The outcomes you posted agree perfectly with constrained molecules, The posted data refereed to un-reliability of g_traj for obtaining of T. I just wanted to know the reason via comparison with g_energy. Those obtained by non-reactive FF of OPLS. but without more details on what you're actually doing, I'm not going to hazard a guess. Recall that even if you set constraints = none, SETTLE is still applied to water molecules unless you use -DFLEXIBLE (which you shouldn't for most normal purposes). My molecules are not water and g_traj gave following T values for same system using two different FFs 1- ReaxFF 0 399.321 1 400.25 2 401.08 3 401.271 4 400.67 5 400.264 6 400.752 7 401.178 8 401.391 9 399.065 10 401.78 As i said already I just converted reaxff trajectory to gro one and also used tpr file (constrain=none in mdp) for estimation of T with g_traj. 2- OPLS 0 269.581 1 271.064 2 271.309 3 271.205 4 271.499 5 270.868 6 272.247 7 271.59 8 271.614 9 270.598 10 271.662 How constrained MD results (OPLS) can be corrected? Rasoul -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] Positive energy .
Why do you think positive values are doubtful? What matters are energy differences between different snapshots The absolute energy is meaningless in the FF framework. Rasoul On Tue, May 13, 2014 at 3:59 PM, Bryan Roessler roess...@uab.edu wrote: Did you hit your nsteps limit? 2 probably isn't enough steps to get below 10 Fmax. *Bryan Roessler | Graduate Research Assistant* UAB | The University of Alabama at Birmingham *uab.edu/cmdb http://uab.edu/cmdb* Knowledge that will change your world On Tue, May 13, 2014 at 8:30 AM, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I am running simulations for a water-CO2 system using the OPLSAA forcefield, where I use TIP4P/Ice water model and the EPM2 model for CO2. After energy minimization I found the value of potential energy to be positive, and also the maximum force value was high (I requested Fmax 10 ). The values are as follows; Potential Energy= 1.7600962e+05 Maximum force = 6.5140656e+01 on atom 1176 Norm of force= 8.7009411e+00 Earlier when I did a simulation for gaseous CO2 using the same model, the potential energies were always positive. But I doubt whether the energy can be positive here. I want to make sure that I am not using any wrong parameters, before I proceed. Please comment. My MDP file is as given below; ; Run control integrator = steep nsteps = 2 ; EM criteria and other stuff emtol = 10 emstep = 0.01 niter= 20 nbfgscorr = 10 ; Output control nstlog = 1 nstenergy = 1 ; Neighborsearching and short-range nonbonded interactions nstlist= 1 ns_type = grid pbc = xyz rlist = 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = switch rvdw-switch =0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft= no ; Temperature and pressure coupling are off during EM tcoupl = no pcoupl = no ; Generate velocities to start gen_vel = no ; options for bonds constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 -- 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] glycated insulin (GROMACS)
See following paper for modelling of initial steps of glycation process protein: http://www.tandfonline.com/doi/abs/10.1080/07391102.2010.10507354#preview For study of advanced glycation end processes, there is nothing to do with emperical FF, you need to use QC approches; see following papers for those, http://pubs.acs.org/doi/abs/10.1021/jp205558d http://link.springer.com/article/10.1007%2Fs00894-011-1161-x http://pubs.acs.org/doi/abs/10.1021/jp2104165 I hope it can help you. Rasoul On Sun, Apr 6, 2014 at 5:01 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/5/14, 11:20 PM, marzieh dehghan wrote: Dear Justin Hi after glycation insulin by autodock, I wan to run it by GROMACS. I would like to know is it possible and correct? I already answered whether or not it's possible. There's nothing to assess in terms of correctness here. -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] conversion of X,Y,Z + velocities to *.trr
Thanks for your replies. 1- I need bond and charge info along with position and velocity ones. All change during the MD simulation required a reactive force field rather than traditional one. 2- How one can construct a tpr for a system in which bonds/charges change when it's evolved? Best, Rasoul On Mon, Dec 23, 2013 at 9:30 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Also, consider what you need it for. If you only need atom/residue information and/or reference coordinates, a .gro/.pdb file will do. Only if you need to have bonds/masses/charges/... you really need a .tpr file for reference. Cheers, Tsjerk On Mon, Dec 23, 2013 at 4:00 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Constructing a .tpr is covered many GROMACS tutorials you can find. What is particular about your case that you do not have one from doing the simulation? Mark On Mon, Dec 23, 2013 at 9:40 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Many thanks Tsjerk, Let me ask another question. As you know in most cases of analysis, one needs to have tpr file along with the trajectory. How can I construct it? The potential that I'm using in my MD simulations is ReaxFF (a reactive FF). Best, Rasoul On Sun, Dec 22, 2013 at 9:21 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Raoul, You can also convert it to .gro or .pdb and do the analysis on that. Scriptwise that's trivial. Cheers, Tsjerk On Sat, Dec 21, 2013 at 10:12 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Dear all, Is there any available script/Tcl in order to convert a x,y,z trajectory (x,y,z-coordinates+velocities) to *.trr one? I have optained the following trajectory and I need to have *.trr for analysing of my MD; C 45.96903 21.49863 24.629130.00.0 0.0 H 47.06603 21.49863 24.629130.00.0 0.0 H 45.80503 22.58663 24.629130.00.0 0.0 H 45.56903 21.09663 25.551130.00.0 0.0 C 45.38203 20.69563 23.470130.00.0 0.0 H 45.90103 19.74763 23.378130.00.0 0.0 H 45.64903 21.18663 22.531130.00.0 0.0 C 43.87003 20.45463 23.584130.00.0 0.0 . . . . Any help is highly appreciated. Best, Rasoul -- 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-usersor 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-usersor 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. -- 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 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
