Re: [gmx-users] pcoupl Berendsen
> A pressure without an error bar is a meaningless value. The fluctuations > of pressure in most systems are on the order of tens or hundreds of bar, > meaning your result is indistinguishable from the target value. To help illustrate this, here is one example of the type of pressure fluctuation you can get. https://twitter.com/dr_dbw/status/968624615063937025 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 9 Nov 2018 at 00:01, Justin Lemkul wrote: > > > > On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote: > > Dear Gromacs users, > > > > In my simulations, I have specified ref_p= 1bar but after MD simulation I > > obtain pressures equal to 0.19 bar (even > > A pressure without an error bar is a meaningless value. The fluctuations > of pressure in most systems are on the order of tens or hundreds of bar, > meaning your result is indistinguishable from the target value. > > > with long simulation times) when using pcoupl=Parrinello-Rahman. I know > > that Parrinello-Rahman is recommend for production runs and Berendsen for > > NPT equilibration. However, I have read in an article that > > Parrinello-Rahman is not stable for low pressures, so in such situations > > its better to use Berendsen. I have tried to use Berendsen for > > I would be interested to know how this "not stable for low pressures" > was determined, because it seems completely unlikely to be true. Most MD > simulations nowadays use Parrinello-Rahman for pressure coupling at 1 > bar/1 atm without any issue if the system is properly equilibrated (and > if not, the problem is with preparation, not the barostat itself). > > > MD simulation but I obtain this Warning and I cannot remove it with the > > -maxwarn option. > > > > "Using Berendsen pressure coupling invalidates the true ensemble for the > > thermostat" > > > > > > How can I use Berendsen for MD simulation? > > Simply, you can't, and you shouldn't. The Berendsen method produces an > invalid statistical mechanical ensemble. It relaxes systems quickly and > is therefore still useful for equilibration, but should never be > employed during data collection. Full stop. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] Gromacs Neighbor List Output
Hello, I noticed that gromacs has an environment variable that seems to allow it to output neighbor lists. I haven't been able to figure out how to use it. Does anyone have an example of how this could work? Thanks, Adriaan Riet -- 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 Decomposition Error
Hello Tom, I got something like decomposition errors when running in GPU clusters, and later I found it is because of PBC unit cell angles. You can try to use trajconv to get out of one pdb file from your simulation box. If the unit cell is non-90degree, it will cause this domain decomposition errors. Thanks, Wenjuan On Thu, Nov 8, 2018 at 10:44 AM tca1 wrote: > Hi everyone, > > I've recently gotten a simulation of a 2D crystal surface set up in > GROMACS using a combination of x2top and periodic-molecules. Things > run okay for me when I do small-scale tests on a single core > (minimization, NVT equilibration, etc), however when I try to scale > this up and run it on multiple processors I get an error saying: > > Not all bonded interactions have been properly assigned to the domain > decomposition cells > > This happens for any number of cores larger than 1, and it happens > even during my minimization step. I don't believe this is the result > of a poor equilibrium geometry, because when I run intermediate-sized > tests on a single core, they finish correctly after only a handful of > steps, even using fairly tight minimization settings. Additionally, > the box itself is simple - just a cube with periodic boundary > conditions applied - and I'm leaving out everything but the crystal > surface in the simulation to reduce the complexity for debugging. > > I suspect the error has something to do with the periodic-molecules > option and an unidentified oversight in my job setup, but I have no > idea where to look. Does anyone have any suggestions? > > Thanks, > Tom Allen > > -- > 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. > -- Best regards Wenjuan Jiang -- 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] Bond Decomposition Error
Hi everyone, I've recently gotten a simulation of a 2D crystal surface set up in GROMACS using a combination of x2top and periodic-molecules. Things run okay for me when I do small-scale tests on a single core (minimization, NVT equilibration, etc), however when I try to scale this up and run it on multiple processors I get an error saying: Not all bonded interactions have been properly assigned to the domain decomposition cells This happens for any number of cores larger than 1, and it happens even during my minimization step. I don't believe this is the result of a poor equilibrium geometry, because when I run intermediate-sized tests on a single core, they finish correctly after only a handful of steps, even using fairly tight minimization settings. Additionally, the box itself is simple - just a cube with periodic boundary conditions applied - and I'm leaving out everything but the crystal surface in the simulation to reduce the complexity for debugging. I suspect the error has something to do with the periodic-molecules option and an unidentified oversight in my job setup, but I have no idea where to look. Does anyone have any suggestions? Thanks, Tom Allen -- 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] pdb2gmx fatal error
Dear Justin, Thank you for your response. Yet, I have not been able to solve the problem. The structure looks fine but gromacs is complaining about a dangling atom at one of the terminal ends, if I choose no terminal to be added. While, assigning a terminal to the ends (which I don't understand why), results to another error, which to me seems bizarre. It is still complaining about an atom (C6) which is not found in the input file (.rtp?), however, it is indeed one of the atoms in the rtp file. Here is what it looks like in the rtp file: [ GLC0 ] [ atoms ] C4 CH1R0.23200 1 O4 OA -0.64200 1 HO4 H 0.41000 1 C3 CH1R0.23200 2 O3OA-0.64200 2 HO3 H 0.41000 2 C2 CH1R0.23200 3 O2OA-0.64200 3 HO2 H 0.41000 3 C6 CH2 0.23200 4 O6OA-0.64200 4 HO6 H 0.41000 4 C5 CH1R0.23200 0 O5OR-0.46400 0 C1 CH1R0.46400 0 O1OE-0.46400 0 And the pdb input file is: ATOM 1 C1 GLC01 3.992 3.199 3.177 1.00 0.04 C ATOM 2 C2 GLC01 3.597 2.204 2.072 1.00 0.04 C ATOM 3 C3 GLC01 4.231 2.633 0.737 1.00 0.04 C ATOM 4 C4 GLC01 3.713 4.036 0.378 1.00 0.04 C ATOM 5 C5 GLC01 4.096 5.017 1.502 1.00 0.04 C ATOM 6 C6 GLC01 3.581 6.419 1.132 1.00 0.04 C ATOM 7 O2 GLC01 4.094 0.828 2.442 1.00 0.04 O ATOM 8 O5 GLC01 3.476 4.569 2.805 1.00 0.04 O ATOM 9 O6 GLC01 4.207 6.834 -0.178 1.00 0.04 O ATOM 10 H1 GLC01 5.128 3.219 3.268 1.00 0.00 H ATOM 11 H2 GLC01 2.462 2.181 1.967 1.00 0.00 H ATOM 12 H3 GLC01 5.366 2.661 0.847 1.00 0.00 H ATOM 13 H4 GLC01 2.578 4.005 0.271 1.00 0.00 H ATOM 14 H5 GLC01 5.230 5.045 1.611 1.00 0.00 H ATOM 15 H61 GLC01 3.858 7.165 1.950 1.00 0.00 H ATOM 16 H62 GLC01 2.449 6.385 1.015 1.00 0.00 H ATOM 17 HO2 GLC01 5.198 0.853 2.551 1.00 0.00 H ATOM 18 HO6 GLC01 5.313 6.850 -0.083 1.00 0.00 H ATOM 19 O4 GLC02 4.312 4.595 9.824 1.00 0.04 O ATOM 20 C1 GLC02 3.708 4.145 8.515 1.00 0.04 C ATOM 21 C2 GLC02 4.109 5.126 7.399 1.00 0.04 C ATOM 22 C3 GLC02 3.497 4.668 6.062 1.00 0.04 C ATOM 23 C4 GLC02 4.005 3.250 5.730 1.00 0.04 C ATOM 24 C5 GLC02 3.616 2.295 6.877 1.00 0.04 C ATOM 25 C6 GLC02 4.151 0.877 6.596 1.00 0.04 C ATOM 26 O2 GLC02 3.601 6.506 7.743 1.00 0.04 O ATOM 27 O3 GLC02 3.909 5.661 5.002 1.00 0.04 O ATOM 28 HO4 GLC02 4.850 3.729 10.263 1.00 0.00 H ATOM 29 O1 GLC01 3.396 2.685 4.467 1.00 0.04 O ATOM 30 O5 GLC02 4.225 2.770 8.173 1.00 0.04 O ATOM 31 O6 GLC02 3.558 0.309 5.328 1.00 0.04 O ATOM 32 H1 GLC02 2.572 4.115 8.609 1.00 0.00 H ATOM 33 H2 GLC02 5.244 5.151 7.307 1.00 0.00 H ATOM 34 H3 GLC02 2.361 4.651 6.153 1.00 0.00 H ATOM 35 H4 GLC02 5.141 3.258 5.636 1.00 0.00 H ATOM 36 H5 GLC02 2.480 2.262 6.979 1.00 0.00 H ATOM 37 H61 GLC02 3.879 0.196 7.468 1.00 0.00 H ATOM 38 H62 GLC02 5.286 0.920 6.494 1.00 0.00 H ATOM 39 HO2 GLC02 2.496 6.480 7.836 1.00 0.00 H ATOM 40 HO3 GLC02 5.015 5.674 4.919 1.00 0.00 H ATOM 41 HO6 GLC02 2.453 0.270 5.418 1.00 0.00 H ATOM 42 O3 GLC01 3.852 1.653 -0.348 1.00 0.00 O ATOM 43 HO3 GLC01 4.305 1.969 -1.311 1.00 0.00 H END The error is given as a result of the command: gmx pdb2gmx -f cellobiose.pdb -o cellobiose.gro -ignh -ter The error: Fatal error: Residue 4 named GLC0 of a molecule in the input file was mapped to an entry in the topology database, but the atom C6 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Do you have any idea why it is happening? Thank you in advanced. Regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: donderdag 8 november 2018 13:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx fatal error On 11/7/18 1:05 PM, Ali Khodayari wrote: > Dear gmx users, > > > > I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom > names
[gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF
Hello Justin I still don't understand where Gromacs takes the x coordinates in the output pmf with g_wham If I run g_wham with tpr-files and pullf-files without the pullx-files -it tpr-files.dat -if pullf-files.dat I get a profile which means that g_wham does not take the X-coordinates in the pullx (I don't give them), but in the tpr files ... So what X-coordinates are stored in the tpr-files ? Then if I use -it tpr-files.dat -ix pullx-files.dat Where does g_wham take the forces and which x coordinates does it take : those from the tpr or those from the pullx ? Moreover when I restart my simulations, I regenerate new tpr files For instance to add 10 more ns gmx convert-tpr -s umbrella10ns.tpr -extend 1 -o umbrella20ns.tpr gmx mdrun -s umbrella20ns.tpr -cpi xxx.cpt If I run g_wham after this simulation, which tpr should I use ? Can you please explain the role of these tpr in g_wham calculations? Thanks a lot On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote: > Hello Justin- > In MY pullx first column is Time and second column is absolute > coordinate of the COM of the pulled group Maybe we are missing an option > which would print X and dX in the pullx files - one of the pull-print stuffs > ???!!.. In that case too bad we would have tons of "bad" pull files Printing > the reaction coordinate (dX) should be the default .. Don't you think so ? > Hence my problem with wham using absolute coordinate instead of actual > distance between the two centers of mass What do you suggest to retrieve the > actual values of my reaction coordinate without rerrunning everything ? It should be straightforward to apply a systematic shift to the values in the output PMF curve. But I don't know how you've set up your pull code to get such output in the first place. The absolute position of group0 should be totally irrelevant. -Justin > Serge > > * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Assigning charge to closely related functional group
Hi All, Following is the structure of the molecule, which I wish to parameterize. CH3 O | || CH3 - C - O - C - | CH3 It is a peptide capping reagent. The last carbon will form bond with the NH2 group of the peptide. I have generated the the topology using PRODRG server and wish to refine the charge group and partial charges as PRODRG server doen't predict them correctly. The closest well-validated structure is of carboxyl ester in the first position of DPPC (or any other glyceride). However there is a minor difference. The carbon attached to three methyl group, in this case is CH0 type and in DPPC it was CH2 type. Since the carbon was part of charge group in DPPC, I fear I may have to change the partial charges. I couldn't find any example where exactly same charge group was used. I will appreciate if anyone can suggest me how to assign correct partial charges. Thanks a lot for the help. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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] DispErsion correction
Dear Justin and Dallas Thank you for your replying I have another problem in minimizing and NVT run of my complex, including a protein and a peptidic ligand which the ligand has 2 phosphotyrosine residues. I generated a topology file of ligand using ff14sb in ambertools 16 and then converted the .inpcrd and .prmtop files in .gro and .top files using acpype python script. The protein topology was generated using amber99sb ff in GROMACS. Then, I cited to gromacs manuscript in order to generate an .itp file of ligand from .top file and generated .itp file by removing the header and footer of .top file in such a way that .itp file starts with : [ moleculetype ] ;namenrexcl mig 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 N3 1 THR N1 0.181200 14.01000 ; qtot 0.181 2H 1 THRH12 0.193400 1.00800 ; qtot 0.375 . . . and ends with 120123122132 1 180.00 4.18400 2 ; C- CD- N-CA 132135134136 1 180.00 43.93200 2 ; CA- O- C- OXT then, modified the complex.gro and .top files according to the tutorials in gromacs, I Minimized the complex by issuing this coomand: gmx grompp -f em.mdp -c solv-ions.gro -p topol.top -o em.tpr gmx mdrun -v -defnm em but noticed that the minimization ended soon : Steepest Descents converged to machine precision in 80 steps, but did not reach the requested Fmax < 1000. Potential Energy = -6.5639856e+05 Maximum force = 7.0647156e+04 on atom 5256 Norm of force = 5.8775842e+02 and when performed the NVT run , faced to this error: starting mdrun 'Protein in water' 20 steps,400.0 ps. step 0 Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.016999, max 0.734404 (between atoms 5258 and 5261) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5258 5261 90.00.0960 0.1665 0.0960 5283 5286 90.00.0960 0.1425 0.0960 Wrote pdb files with previous and current coordinates . . . It should be noted that atoms 5258 and 5261 are related to sol molecules. TIP3P water model was selected for amber99sb force field. Would you please advice and guild me how should I resolve this problem? Thanks in advance Farial these are the .mdp files that I used: em.mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions the nvt.mdp file: title = AMBER NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 20 ; 2 * 20 = 400 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm= lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing =
Re: [gmx-users] start the simulation of the last stopping point.
Hello, you can find information on how to extend simulations here: http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html Cheers Paul On 2018-11-08 14:23, Edjan Silva wrote: Dear fellow scientists, I'm doing a 40ns simulation between DNA and a small molecule. It occurred that around 30 nanoseconds, the computer hung up. How do I start the simulation from the 30 nanoseconds performed? -- 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] start the simulation of the last stopping point.
Dear fellow scientists, I'm doing a 40ns simulation between DNA and a small molecule. It occurred that around 30 nanoseconds, the computer hung up. How do I start the simulation from the 30 nanoseconds performed? -- 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] pcoupl Berendsen
On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote: Dear Gromacs users, In my simulations, I have specified ref_p= 1bar but after MD simulation I obtain pressures equal to 0.19 bar (even A pressure without an error bar is a meaningless value. The fluctuations of pressure in most systems are on the order of tens or hundreds of bar, meaning your result is indistinguishable from the target value. with long simulation times) when using pcoupl=Parrinello-Rahman. I know that Parrinello-Rahman is recommend for production runs and Berendsen for NPT equilibration. However, I have read in an article that Parrinello-Rahman is not stable for low pressures, so in such situations its better to use Berendsen. I have tried to use Berendsen for I would be interested to know how this "not stable for low pressures" was determined, because it seems completely unlikely to be true. Most MD simulations nowadays use Parrinello-Rahman for pressure coupling at 1 bar/1 atm without any issue if the system is properly equilibrated (and if not, the problem is with preparation, not the barostat itself). MD simulation but I obtain this Warning and I cannot remove it with the -maxwarn option. "Using Berendsen pressure coupling invalidates the true ensemble for the thermostat" How can I use Berendsen for MD simulation? Simply, you can't, and you shouldn't. The Berendsen method produces an invalid statistical mechanical ensemble. It relaxes systems quickly and is therefore still useful for equilibration, but should never be employed during data collection. Full stop. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Topology include file "tip3p.itp" not found
On 11/8/18 5:20 AM, Rahma Dahmani wrote: Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro), when i tried to minimize my structure (with grompp) i get this error """ *atomtype OW is not found* then i create manually tip3p.itp file (which contains tip3p parameters) to identify the water atom types and i added in my topology file the following commands: ; Include water topology #include "tip3p.itp" But i always get this error Topology include file "tip3p.itp" not found If you #include a file without a path, grompp looks in the working directory or any directory specified by "include" in the .mdp file. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] DispErsion correction
On 11/7/18 5:06 PM, Dallas Warren wrote: Paper explaining dispersion correct, and what it is: http://dx.doi.org/10.1021/jp0735987 And note that not all force fields are parametrized in such a way that they make use of dispersion correction. -Justin Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Thu, 8 Nov 2018 at 04:51, Farial Tavakoli wrote: Dear gmx users I am trying to simulate my complex using amber99sb ff. There is no amber tutorial in gromacs. I need to know how dispersion correction set in the .mdp files . I can not understand the definitions of DispCorr in mdp option. Should I put it on EnerPres or no ? Would you please clarify me and explain it in short? Thanks in advance Farial -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] combining multiple MD proteins,
On 11/7/18 2:46 PM, daniel madulu shadrack wrote: Dear, I want to combine proteins to merge into single pdb but I get this error below. Command line: gmx trjcat -f 10ns.pdb 15ns.pdb 40ns.pdb 60ns.pdb 90ns.pdb -o all.pdb You don't need trjcat, just use the standard Linux cat to combine text files. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] pcoupl Berendsen
Dear Gromacs users, In my simulations, I have specified ref_p= 1bar but after MD simulation I obtain pressures equal to 0.19 bar (even with long simulation times) when using pcoupl=Parrinello-Rahman. I know that Parrinello-Rahman is recommend for production runs and Berendsen for NPT equilibration. However, I have read in an article that Parrinello-Rahman is not stable for low pressures, so in such situations its better to use Berendsen. I have tried to use Berendsen for MD simulation but I obtain this Warning and I cannot remove it with the -maxwarn option. "Using Berendsen pressure coupling invalidates the true ensemble for the thermostat" How can I use Berendsen for MD simulation? Thanks in advance, C. -- 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] Topology include file "tip3p.itp" not found
Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro), when i tried to minimize my structure (with grompp) i get this error """ *atomtype OW is not found* then i create manually tip3p.itp file (which contains tip3p parameters) to identify the water atom types and i added in my topology file the following commands: ; Include water topology #include "tip3p.itp" But i always get this error Topology include file "tip3p.itp" not found Can you help me please, Thank you ! -- *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des Matériaux à l'état condensé, Laboratoire de Chimie Théorique et Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068, Tunisie Tél: (+216) 28151042* -- 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] Periodic saving of checkpoint file
Hi Mark, Thank you for your answer. I didn't know this option. From what I have read, eneconv is for reading parameters for Nose-Hoover or Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation with the velocity-rescale thermostat or a Langevin dynamics, I don't need the .edr file, right ? Can you please confirm that this is enough to prepare the tpr from the time 50ps of the NVT simulation: gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr -time 50 -p Protein.top -po NVE_mdout.mdp Thank you Le lun. 5 nov. 2018 à 17:50, Mark Abraham a écrit : > Hi, > > Since you are anyway intending to change the ensemble, you can just use > nstxout, nstvout and nstenergy to write output every 10ps. That content is > equivalent to that of the checkpoint. Use trjconv and eneconv afterwards to > split those up, and use them as inputs to grompp -e -t along with the > regular inputs. > > Mark > > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I would like to run a long NVT simulation and save a checkpoint file > every > > 10ps (in order to then run short NVE simulations from each checkpoint). > Is > > there a way to save a .cpt file every 10ps in an automatic way? > > > > I can do it with other program, for example with Amber "ntwr=-5000" will > > save a new restart file every 5000 steps. For now with Gromacs, the only > > thing I have found is to write a loop where at each step I extend the > > simulation time of 10ps with convert-tpr, perform the 10ps simulation, > save > > the .cpt, and then loop again. > > > > Thanks for your help. > > > > Nicolas > > -- > > 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.
