Re: [gmx-users] NPT problem
No, I mean that: 1. Graphene dimensions cannot be exactly 9 x 9. It is a crystal and its in-plane dimensions are _precisely_ determined by the unit cell counts in the corresponding directions. 2. The box size needs to be adjusted in accordance with basic geometry of the crystal and its lattice orientation relative to the rectangular box. 3. With a difference of 2 nm between box size and sample dimensions, there is no way your PBC request is properly processed by x2top. You are likely obtaining a finite sheet instead of a self-passivated periodic sheet and then edges are causing issues. 4. Until you make some effort to learn about graphene and crystals (prior to solvating and doing other things), nothing will work and noone here will be able to help. Alex On Fri, Jul 14, 2017 at 1:09 AM, wrote: > The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean > that the box dimensions are small and thats the problem? > Thanks,Mohammad > From: Alex > To: Discussion list for GROMACS users ; > Discussion list for GROMACS users > Sent: Friday, 14 July 2017, 11:31:06 > Subject: Re: [gmx-users] NPT problem > > > > > > I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT > > -noparam -pbc" for generating the topology. then I used "gmx editconf > > -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating > > the box > > > And where did "-box 11 11 11" come from? For pbc to work the box in your > case has to be a certain size corresponding to the graphene dimensions. > And no, it is not simply its approximate X-Y dimensions. > > Alex > > > > > > > *From:* Alex > > *To:* Discussion list for GROMACS users ; > > Mohammad Roostaie > > *Sent:* Thursday, 13 July 2017, 22:51:48 > > *Subject:* Re: [gmx-users] NPT problem > > > > Also, that tutorial's parameters that are completely wrong for > > graphene. For bulk graphene bond types I suggest: > > > > CJCJ 10.14200 420420.0 > > > > For bulk angles: > > > > CJCJCJ 1 120.000659.346 > > > > For bulk dihedrals: > > > > CJCJCJCJ 3 17.30770 0.0 -17.30770 > > 0.0 0.0 0.0 > > > > These are parameters obtained from a Taylor-expanded optimized > > Tersoff-Brenner potential. Please count the number of bonds and > > dihedrals in your graphene model, as produced by x2top. If the number > > of dihedrals divided by the number of bonds gives you a number, say, > > equal to m, then multiply the dihedral parameters by that number. And > > do NOT use bond constraints -- you are simulating a crystal. > > > > Alex > > > > On Thu, Jul 13, 2017 at 10:45 AM, > <mailto:mohammad.r0...@yahoo.com>> wrote: > > > >Hi All GROMACS users, > > > > > > > >I created graphene with nanotube modeler then I created a force > >field for graphene based on OPLS (by using this link and its > >parameters: http://chembytes.wikidot.com/ grocnt > ><http://chembytes.wikidot.com/grocnt>). I generated the topology > >file using x2top command. I put the graphene inside a box of water > >(TIP3P) which was larger than the graphene dimension with 1000 > > (kJ/mol nm^2) position restraint on all the atoms, and I > >performed the energy minimization and NVT equilibrations (in order > >to get an optimized structure of the graphene for further > >simulations). The results of both of them were good (energy level > >has reached a negative value with the order of 6 and the > >temperature has converged the preferred value). But, when I run > >the NPT equilibration, the results are not good (the pressure and > >density fluctuated very much and the averaged values are so far > >from the preferred ones). Also, during the NPT run, I received > >these messages: > > > > > >step 53965: Water molecule starting at atom 127424 can not be settled. > > > >Check for bad contacts and/or reduce the timestep if appropriate. > > > >Wrote pdb files with previous and current coordinates > > > > > > > >step 141454: Water molecule starting at atom 53366 can not be settled. > > > >Check for bad contacts and/or reduce the timestep if appropriate. > > > >Wrote pdb files with previous and current coordinates > > > > > > > >step 141483: Water molecule starting at atom 53366 can not be settled. > > > &
Re: [gmx-users] NPT problem
The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean that the box dimensions are small and thats the problem? Thanks,Mohammad From: Alex To: Discussion list for GROMACS users ; Discussion list for GROMACS users Sent: Friday, 14 July 2017, 11:31:06 Subject: Re: [gmx-users] NPT problem > > I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT > -noparam -pbc" for generating the topology. then I used "gmx editconf > -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating > the box > And where did "-box 11 11 11" come from? For pbc to work the box in your case has to be a certain size corresponding to the graphene dimensions. And no, it is not simply its approximate X-Y dimensions. Alex > > > *From:* Alex > *To:* Discussion list for GROMACS users ; > Mohammad Roostaie > *Sent:* Thursday, 13 July 2017, 22:51:48 > *Subject:* Re: [gmx-users] NPT problem > > Also, that tutorial's parameters that are completely wrong for > graphene. For bulk graphene bond types I suggest: > > CJ CJ 1 0.14200 420420.0 > > For bulk angles: > > CJ CJ CJ 1 120.000 659.346 > > For bulk dihedrals: > > CJ CJ CJ CJ 3 17.30770 0.0 -17.30770 > 0.0 0.0 0.0 > > These are parameters obtained from a Taylor-expanded optimized > Tersoff-Brenner potential. Please count the number of bonds and > dihedrals in your graphene model, as produced by x2top. If the number > of dihedrals divided by the number of bonds gives you a number, say, > equal to m, then multiply the dihedral parameters by that number. And > do NOT use bond constraints -- you are simulating a crystal. > > Alex > > On Thu, Jul 13, 2017 at 10:45 AM, <mailto:mohammad.r0...@yahoo.com>> wrote: > > Hi All GROMACS users, > > > > I created graphene with nanotube modeler then I created a force > field for graphene based on OPLS (by using this link and its > parameters: http://chembytes.wikidot.com/ grocnt > <http://chembytes.wikidot.com/grocnt>). I generated the topology > file using x2top command. I put the graphene inside a box of water > (TIP3P) which was larger than the graphene dimension with 1000 > (kJ/mol nm^2) position restraint on all the atoms, and I > performed the energy minimization and NVT equilibrations (in order > to get an optimized structure of the graphene for further > simulations). The results of both of them were good (energy level > has reached a negative value with the order of 6 and the > temperature has converged the preferred value). But, when I run > the NPT equilibration, the results are not good (the pressure and > density fluctuated very much and the averaged values are so far > from the preferred ones). Also, during the NPT run, I received > these messages: > > > step 53965: Water molecule starting at atom 127424 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 141454: Water molecule starting at atom 53366 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 141483: Water molecule starting at atom 53366 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323815: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323816: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323818: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355712: Water molecule starting at atom 121748 can not be > settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355714: Water molecule starting at atom 121748 can not be > settled. > > Check for bad contacts and/or reduce the timestep
Re: [gmx-users] NPT problem
I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT -noparam -pbc" for generating the topology. then I used "gmx editconf -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating the box And where did "-box 11 11 11" come from? For pbc to work the box in your case has to be a certain size corresponding to the graphene dimensions. And no, it is not simply its approximate X-Y dimensions. Alex *From:* Alex *To:* Discussion list for GROMACS users ; Mohammad Roostaie *Sent:* Thursday, 13 July 2017, 22:51:48 *Subject:* Re: [gmx-users] NPT problem Also, that tutorial's parameters that are completely wrong for graphene. For bulk graphene bond types I suggest: CJCJ 10.14200 420420.0 For bulk angles: CJ CJ CJ 1 120.000659.346 For bulk dihedrals: CJ CJ CJ CJ 3 17.30770 0.0 -17.30770 0.0 0.0 0.0 These are parameters obtained from a Taylor-expanded optimized Tersoff-Brenner potential. Please count the number of bonds and dihedrals in your graphene model, as produced by x2top. If the number of dihedrals divided by the number of bonds gives you a number, say, equal to m, then multiply the dihedral parameters by that number. And do NOT use bond constraints -- you are simulating a crystal. Alex On Thu, Jul 13, 2017 at 10:45 AM, <mailto:mohammad.r0...@yahoo.com>> wrote: Hi All GROMACS users, I created graphene with nanotube modeler then I created a force field for graphene based on OPLS (by using this link and its parameters: http://chembytes.wikidot.com/ grocnt <http://chembytes.wikidot.com/grocnt>). I generated the topology file using x2top command. I put the graphene inside a box of water (TIP3P) which was larger than the graphene dimension with 1000 (kJ/mol nm^2) position restraint on all the atoms, and I performed the energy minimization and NVT equilibrations (in order to get an optimized structure of the graphene for further simulations). The results of both of them were good (energy level has reached a negative value with the order of 6 and the temperature has converged the preferred value). But, when I run the NPT equilibration, the results are not good (the pressure and density fluctuated very much and the averaged values are so far from the preferred ones). Also, during the NPT run, I received these messages: step 53965: Water molecule starting at atom 127424 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 141454: Water molecule starting at atom 53366 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 141483: Water molecule starting at atom 53366 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 323815: Water molecule starting at atom 30509 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 323816: Water molecule starting at atom 30509 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 323818: Water molecule starting at atom 30509 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 355712: Water molecule starting at atom 121748 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 355714: Water molecule starting at atom 121748 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 355716: Water molecule starting at atom 121748 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 355718: Water molecule starting at atom 121748 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 469414: Water molecule starting at atom 101579 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 469416: Water molecule starting at atom 101579 can not be settled. Check for bad
Re: [gmx-users] NPT problem
Hi Alex, Thank you for your reply. By the term "results were good or not" I meant that whether the temperature, pressure, and density have converged to the preferred values or not (I mentioned it in the parenthesis, too). I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT -noparam -pbc" for generating the topology. then I used "gmx editconf -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating the box then I filled it with water with "gmx solvate -cp gr.gro -cs spc216.gro -o gr_solv.gro -p topol.top" command. The x2top does not require the box dimensions. Should I use the "-pbc" option in editconf, too? Do you mean that first I should perform EM, NVT, NPT, and MD run on the graphene alone without water and any position restraints? Also, I followed the tutorial step by step. Also, I used it since this tutorial is mentioned on Gromacs website. Actually, I think that in this tutorial, the purpose is to generate a force filed for graphene based on OPLS force field. Moreover, I added the ffbonded.itp, ffnonbonded.itp, and tip3p.itp files from OPLS-AA force field to the directory for the water molecules. Also, after optimization of the graphene, I want to put a peptide inside the box, so I should add those files, also I think that I should add the aminoacids.rtp for the peptide in order to use a unique force field for all the molecules and not to use different force fields. Kind regards,Mohammad From: Alex To: Discussion list for GROMACS users ; Mohammad Roostaie Sent: Thursday, 13 July 2017, 22:51:48 Subject: Re: [gmx-users] NPT problem Also, that tutorial's parameters that are completely wrong for graphene. For bulk graphene bond types I suggest: CJ CJ 1 0.14200 420420.0 For bulk angles: CJ CJ CJ 1 120.000 659.346 For bulk dihedrals: CJ CJ CJ CJ 3 17.30770 0.0 -17.30770 0.0 0.0 0.0 These are parameters obtained from a Taylor-expanded optimized Tersoff-Brenner potential. Please count the number of bonds and dihedrals in your graphene model, as produced by x2top. If the number of dihedrals divided by the number of bonds gives you a number, say, equal to m, then multiply the dihedral parameters by that number. And do NOT use bond constraints -- you are simulating a crystal. Alex On Thu, Jul 13, 2017 at 10:45 AM, wrote: Hi All GROMACS users, I created graphene with nanotube modeler then I created a force field for graphene based on OPLS (by using this link and its parameters: http://chembytes.wikidot.com/ grocnt). I generated the topology file using x2top command. I put the graphene inside a box of water (TIP3P) which was larger than the graphene dimension with 1000 (kJ/mol nm^2) position restraint on all the atoms, and I performed the energy minimization and NVT equilibrations (in order to get an optimized structure of the graphene for further simulations). The results of both of them were good (energy level has reached a negative value with the order of 6 and the temperature has converged the preferred value). But, when I run the NPT equilibration, the results are not good (the pressure and density fluctuated very much and the averaged values are so far from the preferred ones). Also, during the NPT run, I received these messages: step 53965: Water molecule starting at atom 127424 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 141454: Water molecule starting at atom 53366 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 141483: Water molecule starting at atom 53366 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 323815: Water molecule starting at atom 30509 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 323816: Water molecule starting at atom 30509 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 323818: Water molecule starting at atom 30509 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 355712: Water molecule starting at atom 121748 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 355714: Water molecule starting at atom 121748 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates
Re: [gmx-users] NPT problem
Also, that tutorial's parameters that are completely wrong for graphene. For bulk graphene bond types I suggest: CJCJ 10.14200 420420.0 For bulk angles: CJ CJ CJ 1 120.000659.346 For bulk dihedrals: CJ CJ CJ CJ 3 17.30770 0.0 -17.30770 0.0 0.0 0.0 These are parameters obtained from a Taylor-expanded optimized Tersoff-Brenner potential. Please count the number of bonds and dihedrals in your graphene model, as produced by x2top. If the number of dihedrals divided by the number of bonds gives you a number, say, equal to m, then multiply the dihedral parameters by that number. And do NOT use bond constraints -- you are simulating a crystal. Alex On Thu, Jul 13, 2017 at 10:45 AM, wrote: > Hi All GROMACS users, > > > > I created graphene with nanotube modeler then I created a force field for > graphene based on OPLS (by using this link and its parameters: > http://chembytes.wikidot.com/grocnt). I generated the topology file using > x2top command. I put the graphene inside a box of water (TIP3P) which was > larger than the graphene dimension with 1000 (kJ/mol nm^2) position > restraint on all the atoms, and I performed the energy minimization and NVT > equilibrations (in order to get an optimized structure of the graphene for > further simulations). The results of both of them were good (energy level > has reached a negative value with the order of 6 and the temperature has > converged the preferred value). But, when I run the NPT equilibration, the > results are not good (the pressure and density fluctuated very much and the > averaged values are so far from the preferred ones). Also, during the NPT > run, I received these messages: > > > step 53965: Water molecule starting at atom 127424 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 141454: Water molecule starting at atom 53366 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 141483: Water molecule starting at atom 53366 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323815: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323816: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323818: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355712: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355714: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355716: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355718: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469414: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469416: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469418: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469420: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > , and a pdb file was saved after each step. > In addition, something interesting is that I performed another run with > all of the previous parameters, except I did not put position restraint on > the graphene, and the results of NPT were good and acceptable, and I did > not get those messages. > > > Can you please help me figure this
Re: [gmx-users] NPT problem
It is very unclear what you mean by "the results were good" and then "the results were not good." Your graphene setup is bad and it propagated to everything else. Please do not start solvating your graphene sample prior to making sure that your model is reasonable. To diagnose what's wrong with your model there isn't enough info. For one, it is unclear if you followed the tutorial correctly. Second, it is unclear if your x2top command was issued on graphene coordinates with the same box size as the solvated box, especially if one resulted in proper PBC and the other did not. Third, you need to turn off all constraints/restraints and first equilibrate graphene in vacuum (EM followed by considerably long NPT at something like 10K) and make absolutely sure that PBC is properly set in-plane, etc, that SP2 bond lengths in graphene are what they are supposed to be. Fourth, do you understand what that CNT tutorial is doing, or are you blindly following it? This stuff requires effort. Noone can help otherwise. Alex On Thu, Jul 13, 2017 at 10:45 AM, wrote: > Hi All GROMACS users, > > > > I created graphene with nanotube modeler then I created a force field for > graphene based on OPLS (by using this link and its parameters: > http://chembytes.wikidot.com/grocnt). I generated the topology file using > x2top command. I put the graphene inside a box of water (TIP3P) which was > larger than the graphene dimension with 1000 (kJ/mol nm^2) position > restraint on all the atoms, and I performed the energy minimization and NVT > equilibrations (in order to get an optimized structure of the graphene for > further simulations). The results of both of them were good (energy level > has reached a negative value with the order of 6 and the temperature has > converged the preferred value). But, when I run the NPT equilibration, the > results are not good (the pressure and density fluctuated very much and the > averaged values are so far from the preferred ones). Also, during the NPT > run, I received these messages: > > > step 53965: Water molecule starting at atom 127424 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 141454: Water molecule starting at atom 53366 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 141483: Water molecule starting at atom 53366 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323815: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323816: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 323818: Water molecule starting at atom 30509 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355712: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355714: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355716: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 355718: Water molecule starting at atom 121748 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469414: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469416: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469418: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > step 469420: Water molecule starting at atom 101579 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > , and a pdb file was saved after each step. > In addi
