[gmx-users] Re: Positive Potential Energy after equilibration
Dear Users, I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen bond distance using g_hbond and it comes to 0.267 nm. I've also calculated the density and it comes to 1229 kg/m3 (solid density = 1120 kg/m3 at 300 K !!! Comments please...). I wanted to know if there are other properties that can be calculated to validate my simulations. Justin in his paper J. Chem. Inf. Model. 2010, 50, 2221–2235, talked about calculating the enthalpy of vaporization using the formula ∆Hvap = 〈Egas〉 - 〈Eliquid〉 + RT I wanted to know how to apply this in simulation? Assuming I know the boiling, do i simulate at that temperature until liquid becomes vapor? How will I know that the liquid has vaporized. Thank you so much for all your help. -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998541.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Positive Potential Energy after equilibration
On 6/15/12 4:08 AM, Satish Kamath wrote: Dear Users, I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen bond distance using g_hbond and it comes to 0.267 nm. I've also calculated the density and it comes to 1229 kg/m3 (solid density = 1120 kg/m3 at 300 K !!! Comments please...). It seems that your model is rather poor. If your liquid is more dense than your solid (and you're not water!) then it's not a very good representation. I wanted to know if there are other properties that can be calculated to validate my simulations. Justin in his paper J. Chem. Inf. Model. 2010, 50, 2221–2235, talked about calculating the enthalpy of vaporization using the formula ∆Hvap = 〈Egas〉 - 〈Eliquid〉 + RT I wanted to know how to apply this in simulation? Assuming I know the boiling, do i simulate at that temperature until liquid becomes vapor? How will I know that the liquid has vaporized. The calculation above does not imply that you cause the liquid to boil. You need two simulations - liquid (condensed) and gas. The details of what we did are in the paper and in the Gromos96 references that have been published over the years. This topic has also been discussed at length in the mailing list archive, so I would encourage you to look for the threads. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive Potential Energy after equilibration
Dear Sir, I removed the H-H 1-4 interaction from pairs and this seems to have lowered the potential a lot to 10^2 from 9000 but is still positive. But is it a valid thing to do? Satish Kamath IISc Bangalore India -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998429.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Positive Potential Energy after equilibration
On 6/13/12 4:29 AM, Satish Kamath wrote: Dear Sir, I removed the H-H 1-4 interaction from pairs and this seems to have lowered the potential a lot to 10^2 from 9000 but is still positive. But is it a valid thing to do? Haphazardly deleting energetic terms to produce a more desirable energy is a poor strategy for parameterization. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive Potential Energy after equilibration
I've refined the charge distribution. nr type resnr resid atom cgnr charge- prodrg (NEW)mass 1OA 1 F09 OAD 1 -0.117 (-0.596) 15.9994 2 H 1 F09 HAD 10.027 (+0.469) 1.0080 3 C 1 F09 CAC 10.078 (+0.274) 12.0110 4 CR1 1 F09 CAF 1 -0.005 (-0.390) 12.0110 5HC 1 F09 HAF 10.014 (+0.195) 1.0080 6 C 1 F09 CAH 1 -0.014 (+0.104) 12.0110 7 CR1 1 F09 CAI 1 -0.006 (-0.197) 12.0110 8HC 1 F09 HAI 10.014 (+0.140) 1.0080 9 CR1 1 F09 CAK 1 -0.005 (-0.139) 12.0110 10HC 1 F09 HAK 10.014 (+0.139) 1.0080 11 CR1 1 F09 CAL 2 -0.006 (-0.139) 12.0110 12HC 1 F09 HAL 20.014 (+0.139) 1.0080 13 CR1 1 F09 CAJ 2 -0.005 (-0.197) 12.0110 14HC 1 F09 HAJ 20.014 (+0.140) 1.0080 15 C 1 F09 CAG 2 -0.014 (+0.104) 12.0110 16 CR1 1 F09 CAA 2 -0.005 (-0.390) 12.0110 17HC 1 F09 HAA 20.013 (+0.195) 1.0080 18 C 1 F09 CAB 20.078 (+0.274) 12.0110 19OA 1 F09 OAE 2 -0.116 (-0.594) 15.9994 20 H 1 F09 HAE 20.027 (+0.469) 1.0080 The ones in the bracket are the new charges applied. These are from the Automated Topology Builder which does the QM calculations. They seemed more appropriate as they match with the ones on p-cresol in the paper. I did not modify the bond parameters from PRODRG as suggested by the paper. The potential energy has reduced and is arnd 1.5e+04 but is still positive. Can I get some help with this? Thank you for all the help in advance. :) Satish Kamath IISc Bangalore -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998362.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Positive Potential Energy after equilibration
On 6/12/12 4:13 AM, Satish Kamath wrote: I've refined the charge distribution. nr type resnr resid atom cgnr charge- prodrg (NEW) mass 1OA 1 F09 OAD 1 -0.117 (-0.596)15.9994 2 H 1 F09 HAD 10.027 (+0.469)1.0080 3 C 1 F09 CAC 10.078 (+0.274)12.0110 4 CR1 1 F09 CAF 1 -0.005 (-0.390)12.0110 5HC 1 F09 HAF 10.014 (+0.195)1.0080 6 C 1 F09 CAH 1 -0.014 (+0.104)12.0110 7 CR1 1 F09 CAI 1 -0.006 (-0.197)12.0110 8HC 1 F09 HAI 10.014 (+0.140)1.0080 9 CR1 1 F09 CAK 1 -0.005 (-0.139)12.0110 10HC 1 F09 HAK 10.014 (+0.139)1.0080 11 CR1 1 F09 CAL 2 -0.006 (-0.139)12.0110 12HC 1 F09 HAL 20.014 (+0.139)1.0080 13 CR1 1 F09 CAJ 2 -0.005 (-0.197)12.0110 14HC 1 F09 HAJ 20.014 (+0.140)1.0080 15 C 1 F09 CAG 2 -0.014 (+0.104)12.0110 16 CR1 1 F09 CAA 2 -0.005 (-0.390)12.0110 17HC 1 F09 HAA 20.013 (+0.195)1.0080 18 C 1 F09 CAB 20.078 (+0.274)12.0110 19OA 1 F09 OAE 2 -0.116 (-0.594)15.9994 20 H 1 F09 HAE 20.027 (+0.469)1.0080 The ones in the bracket are the new charges applied. These are from the Automated Topology Builder which does the QM calculations. They seemed more appropriate as they match with the ones on p-cresol in the paper. I did not modify the bond parameters from PRODRG as suggested by the paper. The potential energy has reduced and is arnd 1.5e+04 but is still positive. Can I get some help with this? Thank you for all the help in advance. :) Those charges certainly do look better. How long are your simulations? It may take quite a while for your system to rearrange and equilibrate appropriately. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive Potential Energy after equilibration
Dear Sir, Thank you for your reply. I just ran NPT and the potential stabilizes at around +9000. The charge distribution change has reduced a lot of potential but it is still positive. My NPT ran for 1ns. Satish Kamath IISc Bangalore -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998389.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Positive Potential Energy after equilibration
On 6/12/12 8:26 AM, Satish Kamath wrote: Dear Sir, Thank you for your reply. I just ran NPT and the potential stabilizes at around +9000. The charge distribution change has reduced a lot of potential but it is still positive. My NPT ran for 1ns. Then either the topology is still not suitable or the simulation is not long enough. Make sure you're analyzing other observables to judge the quality of your model (RDF, H-bonding, density, etc). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive Potential Energy after equilibration
Dear Sir, Thank you once again for your reply. I ran the simulation longer. The potential energy has stabilized to around 9000 and does not show a decreasing trend. Also the max hydrogen bond distance is around 0.3 nm. The density of the solid is 1120 kg/m3, couldn't get the density data after its melting point. The calculated density at 450 K and 1 bar from the simulation comes to 1200 kg/m3. Well all this could mean that the topology parameters are not appropriate. Satish Kamath IISc Bangalore India -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998404.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive Potential Energy after equilibration
Dear Sir, Thank you for your response. I've read the paper and will look into the charge distribution. Thank you once again. Satish Kamath IISc Bangalore India -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998337.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: positive potential energy
Sorry ...I forget to announce that my potential energy is positive, is it logical? From: Zahra M s_zahra_mous...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December 29, 2011 12:52 PM Subject: positive potential energy Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: positive potential energy
On 29/12/2011 8:24 PM, Zahra M wrote: Sorry ...I forget to announce that my potential energy is positive, is it logical? No. *From:* Zahra M s_zahra_mous...@yahoo.com *To:* gmx-users@gromacs.org gmx-users@gromacs.org *Sent:* Thursday, December 29, 2011 12:52 PM *Subject:* positive potential energy Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. It's not an error, but an advisory about your performance, and doesn't matter for EM in vacuo which will only run for a few seconds. Using a plain cut-off is unreasonable by definition, but doesn't matter for EM in vacuo. Otherwise, you should note that the suggestion is to increase the cut-off *and* the PME grid spacing, not just one of them. Mark thank you in advanced Bests -Zahra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive potential energy for TFE solvent
Hi Mark, Thanks for the quick reply. But i have already done what u suggested. On 15/11/2011 6:06 PM, Harpreet Basra wrote: Hi I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. *tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H and to construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. That link says Work out how much volume a single molecule would have in the box of your chosen density and size. Useeditconf http://www.gromacs.org/editconfto place a box of that size around your single molecule. It does not seem to me that you have done this. Mark I did place the *single molecule* in a box of size required to get a density of 1383 g/L. I also checked the density of the solvent box (containing 216 molecules after NVT equilibration for 200 ps) I constructed the average value comes out to be 1397 g/L with a std deviation of 30 g/L, thus it seems range. Moreover, the potential energy of this one molecule (tfe.gro) was coming out to be highly negative (-6.4E+08 kJ/mol). But on generating a solvent system with 216 TFE molecules the energy becomes (1.9E+04 kJ/mol). Harpreet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Positive potential energy for TFE solvent
On 16/11/2011 1:18 AM, Harpreet Basra wrote: Hi Mark, Thanks for the quick reply. But i have already done what u suggested. On 15/11/2011 6:06 PM, Harpreet Basra wrote: Hi I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. *tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H and to construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. That link says Work out how much volume a single molecule would have in the box of your chosen density and size. Useeditconf http://www.gromacs.org/editconfto place a box of that size around your single molecule. It does not seem to me that you have done this. Mark I did place the *single molecule* in a box of size required to get a density of 1383 g/L. I also checked the density of the solvent box (containing 216 molecules after NVT equilibration for 200 ps) I constructed the average value comes out to be 1397 g/L with a std deviation of 30 g/L, thus it seems range. Moreover, the potential energy of this one molecule (tfe.gro) was coming out to be highly negative
[gmx-users] Re: Positive potential energy for TFE solvent
hi, I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. the energy of this one molecule (tfe.gro) was coming out to b e highly negative (-6.4E+08 kJ/mol). But on generating a solvent system with 216 molecules the energy becomes (1.9E+04 kJ/mol). **tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H To construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. Though i checked the denity of solvent box i constructed the average valu comes out to be 1397g/L with a std deviation of 30g/L. thus it seems range. thanks Harpreet 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? You probably have atomic overlaps from your choice of cubic 0.516 box earlier. Did you look at the results of genconf before computing with them? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
