Re: [gmx-users] positive potential energy
Den 2020-03-15 kl. 20:53, skrev Afsane Farhadi: hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased but had a positive value . is my simulation wrong ? help me please Sent from Yahoo Mail on Android No. I just answered a similar question. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] positive potential energy
hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased but had a positive value . is my simulation wrong ? help me please Sent from Yahoo Mail on Android -- 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 potential energy
Hi, Thanks for your help, Justin! Regards, Mahsa On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul wrote: > > > On 2/25/18 10:15 AM, Mahsa wrote: > >> Dear Justin, >> >> Thank you for your reply! >> >> In general, is it a good approach to first use steep algorithm for EM and >> then to further minimize do EM with cg algorithm, on the output structure? >> > > I usually don't find multiple steps of EM needed in most cases, but > occasionally. The purpose of EM is to find a plausible starting point for > the simulation - you can never know if you're in the global minimum so it's > a bit of working in the dark, anyway. But the gradient (max force) reports > on that. > > Could you please comment on my question about the mdp files and pbc as >> well? Actually, you mentioned here: >> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users >> /2017-February/111219.html >> >> that for one chain of polymer in vacuum, pbc should not be considered. So, >> for my simulation, in the first step I have one chain in vaccum and >> eventually I want to pack the whole box with polymer chains and ions, >> should I use pbc or not and which of the mdp files in my first post is >> correct? >> > > If you're working in the condensed phase, you need finite cutoffs, PME, > and PBC. > > -Justin > > > Regards, >> Mahsa >> >> On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul wrote: >> >> >>> On 2/25/18 9:26 AM, Mahsa wrote: >>> >>> Dear Mark, Thank you for your reply. However, this is not clear for me yet since I read this in the tutorial from Justin: "There are two very important factors to evaluate and determine if EM was successful. The first is the potential energy (printed at the end of the EM process, even without -v). Epot should be negative. The second important feature is the maximum force, Fmax, the target for which was set in minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than 1000 kJ mol-1 nm-1." So I don't know whether it is correct to continue a simulation which gives positive potential energy after the energy minimisation or not? And also as I mentioned in my first post (the two different mdp files), I don't know if I should consider pbc or not, in my simulation. Unfortunately, I didn't understand your answer to my previous questions. Do you mean that the steep integrator is not good to do energy minimization for this type of simulation? Would you please help me to fix these problems? There is no problem. You're just comparing apples and oranges. >>> >>> The tutorial system is a simple protein solvated by lots of water. The >>> potential energy function is the sum of bonded and nonbonded terms. In an >>> aqueous protein system, the nonbonded terms (particularly water-water >>> electrostatics) dominate the potential energy via favorable hydrogen bond >>> interactions. The internal (bonded) parameters for all the other species >>> are small in magnitude, by comparison, so the nonbonded terms dominate >>> and >>> you get a negative potential energy. >>> >>> In your case, you have comparatively weak nonbonded terms and larger >>> bonded terms, such that the potential energy function is dominated by >>> internal energy, which is by definition, positive. >>> >>> This is not an indication that anything is wrong with the algorithms >>> used. >>> >>> -Justin >>> >>> >>> Regards, >>> Mahsa On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham >>> > wrote: Hi, > Even if there are minima on the surface that have negative energy > (which > will depend how the model was developed, which you should look into) > there's no reason to expect an arbitrary starting configuration will > find > one after a steepest descent search. A tangled pile of strings will > stay > tangled. > > Mark > > On Fri, Feb 23, 2018, 23:28 Mahsa E wrote: > > Hello, > >> I want to simulate a box of polymer (32 chains) with salt. I started >> with >> one chain of the polymer in the box. However, after the energy >> minimisation, the energy is still positive. I found the discussion in >> the >> link below very similar to the problem I have: >> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users >> /2017-February/111219.html >> >> and tried the tips from Justin in the link but I still get positive >> >> energy. > > This is my first MDP file: >> >> define = >> integrator = steep >> nsteps = -1 >> nstcgsteep = 10 >> constraints = none >> lincs_order = 8 >> emtol= 20 >> emstep = 0.01 >> comm-mode= Linear >> nstcomm = 1 >> nstcalcen
Re: [gmx-users] Positive potential energy
On 2/25/18 10:15 AM, Mahsa wrote: Dear Justin, Thank you for your reply! In general, is it a good approach to first use steep algorithm for EM and then to further minimize do EM with cg algorithm, on the output structure? I usually don't find multiple steps of EM needed in most cases, but occasionally. The purpose of EM is to find a plausible starting point for the simulation - you can never know if you're in the global minimum so it's a bit of working in the dark, anyway. But the gradient (max force) reports on that. Could you please comment on my question about the mdp files and pbc as well? Actually, you mentioned here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html that for one chain of polymer in vacuum, pbc should not be considered. So, for my simulation, in the first step I have one chain in vaccum and eventually I want to pack the whole box with polymer chains and ions, should I use pbc or not and which of the mdp files in my first post is correct? If you're working in the condensed phase, you need finite cutoffs, PME, and PBC. -Justin Regards, Mahsa On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul wrote: On 2/25/18 9:26 AM, Mahsa wrote: Dear Mark, Thank you for your reply. However, this is not clear for me yet since I read this in the tutorial from Justin: "There are two very important factors to evaluate and determine if EM was successful. The first is the potential energy (printed at the end of the EM process, even without -v). Epot should be negative. The second important feature is the maximum force, Fmax, the target for which was set in minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than 1000 kJ mol-1 nm-1." So I don't know whether it is correct to continue a simulation which gives positive potential energy after the energy minimisation or not? And also as I mentioned in my first post (the two different mdp files), I don't know if I should consider pbc or not, in my simulation. Unfortunately, I didn't understand your answer to my previous questions. Do you mean that the steep integrator is not good to do energy minimization for this type of simulation? Would you please help me to fix these problems? There is no problem. You're just comparing apples and oranges. The tutorial system is a simple protein solvated by lots of water. The potential energy function is the sum of bonded and nonbonded terms. In an aqueous protein system, the nonbonded terms (particularly water-water electrostatics) dominate the potential energy via favorable hydrogen bond interactions. The internal (bonded) parameters for all the other species are small in magnitude, by comparison, so the nonbonded terms dominate and you get a negative potential energy. In your case, you have comparatively weak nonbonded terms and larger bonded terms, such that the potential energy function is dominated by internal energy, which is by definition, positive. This is not an indication that anything is wrong with the algorithms used. -Justin Regards, Mahsa On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham wrote: Hi, Even if there are minima on the surface that have negative energy (which will depend how the model was developed, which you should look into) there's no reason to expect an arbitrary starting configuration will find one after a steepest descent search. A tangled pile of strings will stay tangled. Mark On Fri, Feb 23, 2018, 23:28 Mahsa E wrote: Hello, I want to simulate a box of polymer (32 chains) with salt. I started with one chain of the polymer in the box. However, after the energy minimisation, the energy is still positive. I found the discussion in the link below very similar to the problem I have: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html and tried the tips from Justin in the link but I still get positive energy. This is my first MDP file: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol= 20 emstep = 0.01 comm-mode= Linear nstcomm = 1 nstcalcenergy= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ns_type = grid cutoff-scheme= verlet coulombtype = PME nstlist = 10 rlist= 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = xyz and this is the second one which I tried to follow the tips from the link mentioned above: define = integrator = steep nsteps = -1 nstcgsteep = 10 con
Re: [gmx-users] Positive potential energy
Dear Justin, Thank you for your reply! In general, is it a good approach to first use steep algorithm for EM and then to further minimize do EM with cg algorithm, on the output structure? Could you please comment on my question about the mdp files and pbc as well? Actually, you mentioned here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html that for one chain of polymer in vacuum, pbc should not be considered. So, for my simulation, in the first step I have one chain in vaccum and eventually I want to pack the whole box with polymer chains and ions, should I use pbc or not and which of the mdp files in my first post is correct? Regards, Mahsa On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul wrote: > > > On 2/25/18 9:26 AM, Mahsa wrote: > >> Dear Mark, >> >> Thank you for your reply. However, this is not clear for me yet since I >> read this in the tutorial from Justin: >> >> "There are two very important factors to evaluate and determine if EM was >> successful. The first is the potential energy (printed at the end of the >> EM >> process, even without -v). Epot should be negative. The second important >> feature is the maximum force, Fmax, the target for which was set in >> minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than >> 1000 kJ mol-1 nm-1." >> >> So I don't know whether it is correct to continue a simulation which gives >> positive potential energy after the energy minimisation or not? >> >> And also as I mentioned in my first post (the two different mdp files), I >> don't know if I should consider pbc or not, in my simulation. >> >> Unfortunately, I didn't understand your answer to my previous questions. >> Do >> you mean that the steep integrator is not good to do energy minimization >> for this type of simulation? >> >> Would you please help me to fix these problems? >> > > There is no problem. You're just comparing apples and oranges. > > The tutorial system is a simple protein solvated by lots of water. The > potential energy function is the sum of bonded and nonbonded terms. In an > aqueous protein system, the nonbonded terms (particularly water-water > electrostatics) dominate the potential energy via favorable hydrogen bond > interactions. The internal (bonded) parameters for all the other species > are small in magnitude, by comparison, so the nonbonded terms dominate and > you get a negative potential energy. > > In your case, you have comparatively weak nonbonded terms and larger > bonded terms, such that the potential energy function is dominated by > internal energy, which is by definition, positive. > > This is not an indication that anything is wrong with the algorithms used. > > -Justin > > > Regards, >> Mahsa >> >> On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham >> wrote: >> >> Hi, >>> >>> Even if there are minima on the surface that have negative energy (which >>> will depend how the model was developed, which you should look into) >>> there's no reason to expect an arbitrary starting configuration will find >>> one after a steepest descent search. A tangled pile of strings will stay >>> tangled. >>> >>> Mark >>> >>> On Fri, Feb 23, 2018, 23:28 Mahsa E wrote: >>> >>> Hello, I want to simulate a box of polymer (32 chains) with salt. I started with one chain of the polymer in the box. However, after the energy minimisation, the energy is still positive. I found the discussion in the link below very similar to the problem I have: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html and tried the tips from Justin in the link but I still get positive >>> energy. >>> This is my first MDP file: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol= 20 emstep = 0.01 comm-mode= Linear nstcomm = 1 nstcalcenergy= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ns_type = grid cutoff-scheme= verlet coulombtype = PME nstlist = 10 rlist= 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = xyz and this is the second one which I tried to follow the tips from the link mentioned above: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints
Re: [gmx-users] Positive potential energy
On 2/25/18 9:26 AM, Mahsa wrote: Dear Mark, Thank you for your reply. However, this is not clear for me yet since I read this in the tutorial from Justin: "There are two very important factors to evaluate and determine if EM was successful. The first is the potential energy (printed at the end of the EM process, even without -v). Epot should be negative. The second important feature is the maximum force, Fmax, the target for which was set in minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than 1000 kJ mol-1 nm-1." So I don't know whether it is correct to continue a simulation which gives positive potential energy after the energy minimisation or not? And also as I mentioned in my first post (the two different mdp files), I don't know if I should consider pbc or not, in my simulation. Unfortunately, I didn't understand your answer to my previous questions. Do you mean that the steep integrator is not good to do energy minimization for this type of simulation? Would you please help me to fix these problems? There is no problem. You're just comparing apples and oranges. The tutorial system is a simple protein solvated by lots of water. The potential energy function is the sum of bonded and nonbonded terms. In an aqueous protein system, the nonbonded terms (particularly water-water electrostatics) dominate the potential energy via favorable hydrogen bond interactions. The internal (bonded) parameters for all the other species are small in magnitude, by comparison, so the nonbonded terms dominate and you get a negative potential energy. In your case, you have comparatively weak nonbonded terms and larger bonded terms, such that the potential energy function is dominated by internal energy, which is by definition, positive. This is not an indication that anything is wrong with the algorithms used. -Justin Regards, Mahsa On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham wrote: Hi, Even if there are minima on the surface that have negative energy (which will depend how the model was developed, which you should look into) there's no reason to expect an arbitrary starting configuration will find one after a steepest descent search. A tangled pile of strings will stay tangled. Mark On Fri, Feb 23, 2018, 23:28 Mahsa E wrote: Hello, I want to simulate a box of polymer (32 chains) with salt. I started with one chain of the polymer in the box. However, after the energy minimisation, the energy is still positive. I found the discussion in the link below very similar to the problem I have: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html and tried the tips from Justin in the link but I still get positive energy. This is my first MDP file: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol= 20 emstep = 0.01 comm-mode= Linear nstcomm = 1 nstcalcenergy= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ns_type = grid cutoff-scheme= verlet coulombtype = PME nstlist = 10 rlist= 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = xyz and this is the second one which I tried to follow the tips from the link mentioned above: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol= 20 emstep = 0.01 comm-mode= Linear nstcomm = 1 nstcalcenergy= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ns_type = grid cutoff-scheme= group coulombtype = cut-off nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no My questions are: - I'm not sure if either of these MDP files are correct for the system I'm trying to simulate? - Why energy is positive in this simulation? Is there something fundamentally wrong in the simulation which I'm not aware of? Regards, Mahsa -- 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
Re: [gmx-users] Positive potential energy
Dear Mark, Thank you for your reply. However, this is not clear for me yet since I read this in the tutorial from Justin: "There are two very important factors to evaluate and determine if EM was successful. The first is the potential energy (printed at the end of the EM process, even without -v). Epot should be negative. The second important feature is the maximum force, Fmax, the target for which was set in minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than 1000 kJ mol-1 nm-1." So I don't know whether it is correct to continue a simulation which gives positive potential energy after the energy minimisation or not? And also as I mentioned in my first post (the two different mdp files), I don't know if I should consider pbc or not, in my simulation. Unfortunately, I didn't understand your answer to my previous questions. Do you mean that the steep integrator is not good to do energy minimization for this type of simulation? Would you please help me to fix these problems? Regards, Mahsa On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham wrote: > Hi, > > Even if there are minima on the surface that have negative energy (which > will depend how the model was developed, which you should look into) > there's no reason to expect an arbitrary starting configuration will find > one after a steepest descent search. A tangled pile of strings will stay > tangled. > > Mark > > On Fri, Feb 23, 2018, 23:28 Mahsa E wrote: > > > Hello, > > > > I want to simulate a box of polymer (32 chains) with salt. I started with > > one chain of the polymer in the box. However, after the energy > > minimisation, the energy is still positive. I found the discussion in the > > link below very similar to the problem I have: > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users > > /2017-February/111219.html > > > > and tried the tips from Justin in the link but I still get positive > energy. > > > > This is my first MDP file: > > > > define = > > integrator = steep > > nsteps = -1 > > nstcgsteep = 10 > > constraints = none > > lincs_order = 8 > > emtol= 20 > > emstep = 0.01 > > comm-mode= Linear > > nstcomm = 1 > > nstcalcenergy= 1 > > ; Output frequency for energies to log file and energy file > > nstlog = 1 > > nstenergy= 1 > > ns_type = grid > > cutoff-scheme= verlet > > coulombtype = PME > > nstlist = 10 > > rlist= 1.0 > > rcoulomb = 1.0 > > rvdw = 1.0 > > Tcoupl = no > > Pcoupl = no > > gen_vel = no > > nstxout = 1 > > pbc = xyz > > > > and this is the second one which I tried to follow the tips from the link > > mentioned above: > > > > define = > > integrator = steep > > nsteps = -1 > > nstcgsteep = 10 > > constraints = none > > lincs_order = 8 > > emtol= 20 > > emstep = 0.01 > > comm-mode= Linear > > nstcomm = 1 > > nstcalcenergy= 1 > > ; Output frequency for energies to log file and energy file > > nstlog = 1 > > nstenergy= 1 > > ns_type = grid > > cutoff-scheme= group > > coulombtype = cut-off > > nstlist = 0 > > rlist= 0 > > rcoulomb = 0 > > rvdw = 0 > > Tcoupl = no > > Pcoupl = no > > gen_vel = no > > nstxout = 1 > > pbc = no > > > > My questions are: > > > > - I'm not sure if either of these MDP files are correct for the system > I'm > > trying to simulate? > > > > - Why energy is positive in this simulation? Is there something > > fundamentally wrong in the simulation which I'm not aware of? > > > > Regards, > > Mahsa > > -- > > 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...
Re: [gmx-users] Positive potential energy
Hi, Even if there are minima on the surface that have negative energy (which will depend how the model was developed, which you should look into) there's no reason to expect an arbitrary starting configuration will find one after a steepest descent search. A tangled pile of strings will stay tangled. Mark On Fri, Feb 23, 2018, 23:28 Mahsa E wrote: > Hello, > > I want to simulate a box of polymer (32 chains) with salt. I started with > one chain of the polymer in the box. However, after the energy > minimisation, the energy is still positive. I found the discussion in the > link below very similar to the problem I have: > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users > /2017-February/111219.html > > and tried the tips from Justin in the link but I still get positive energy. > > This is my first MDP file: > > define = > integrator = steep > nsteps = -1 > nstcgsteep = 10 > constraints = none > lincs_order = 8 > emtol= 20 > emstep = 0.01 > comm-mode= Linear > nstcomm = 1 > nstcalcenergy= 1 > ; Output frequency for energies to log file and energy file > nstlog = 1 > nstenergy= 1 > ns_type = grid > cutoff-scheme= verlet > coulombtype = PME > nstlist = 10 > rlist= 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > Tcoupl = no > Pcoupl = no > gen_vel = no > nstxout = 1 > pbc = xyz > > and this is the second one which I tried to follow the tips from the link > mentioned above: > > define = > integrator = steep > nsteps = -1 > nstcgsteep = 10 > constraints = none > lincs_order = 8 > emtol= 20 > emstep = 0.01 > comm-mode= Linear > nstcomm = 1 > nstcalcenergy= 1 > ; Output frequency for energies to log file and energy file > nstlog = 1 > nstenergy= 1 > ns_type = grid > cutoff-scheme= group > coulombtype = cut-off > nstlist = 0 > rlist= 0 > rcoulomb = 0 > rvdw = 0 > Tcoupl = no > Pcoupl = no > gen_vel = no > nstxout = 1 > pbc = no > > My questions are: > > - I'm not sure if either of these MDP files are correct for the system I'm > trying to simulate? > > - Why energy is positive in this simulation? Is there something > fundamentally wrong in the simulation which I'm not aware of? > > Regards, > Mahsa > -- > 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] Positive potential energy
Hello, I want to simulate a box of polymer (32 chains) with salt. I started with one chain of the polymer in the box. However, after the energy minimisation, the energy is still positive. I found the discussion in the link below very similar to the problem I have: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users /2017-February/111219.html and tried the tips from Justin in the link but I still get positive energy. This is my first MDP file: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol= 20 emstep = 0.01 comm-mode= Linear nstcomm = 1 nstcalcenergy= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ns_type = grid cutoff-scheme= verlet coulombtype = PME nstlist = 10 rlist= 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = xyz and this is the second one which I tried to follow the tips from the link mentioned above: define = integrator = steep nsteps = -1 nstcgsteep = 10 constraints = none lincs_order = 8 emtol= 20 emstep = 0.01 comm-mode= Linear nstcomm = 1 nstcalcenergy= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ns_type = grid cutoff-scheme= group coulombtype = cut-off nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no My questions are: - I'm not sure if either of these MDP files are correct for the system I'm trying to simulate? - Why energy is positive in this simulation? Is there something fundamentally wrong in the simulation which I'm not aware of? Regards, Mahsa -- 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 potential energy
Hi, On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati wrote: > Hi all > I run two simulations on a 16 aa peptide under the same conditions > (forcefield, simulation duration, ...) except the solvent in one of > the simulations was TFE instead of water. The potential energy in the TFE > containing system was positive (about 14 Kj/mol), while in water > containing system was negative (about -7 Kj/mol). Is it normal? or some > kind of error has occurred? > Seems normal. Models are typically not parameterized to have meaningful total energies (but the differences and gradients are useful). Mark > -- > 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] positive potential energy
Hi all I run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? -- 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] Positive potential energy
Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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] Positive potential energy
Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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] Positive potential energy
Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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 Potential Energy.
Hey Daniel :) This doesn’t make sense as the molecule should fly apart with always > positive PE. > > You need a force to make things fly apart, but the force has little to do with the absolute PE. It's the gradients that do it. And as Justin points out, your system can choose between positive PE and even more positive PE. Cheers, Tsjerk -- 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.
Re: [gmx-users] Positive Potential Energy.
On 8/28/14, 2:04 PM, Dan Sponseller wrote: Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation. Bond energy can only ever be zero (all bonds at exactly equilibrium values) or positive (not equilibrium values). I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE. I have tried gromos ff and opsla ff. Both do this. A colleague of mine also gets this with his simulations although he reports negative potential when solvated. Negative potentials in condensed phase systems occur because of the massive amount of favorable nonbonded interactions, particularly hydrogen bonding between waters and with solute. Any help would be appreciated or any explanation on how to interpret gromacs output on this. I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system. What is the system? Positive energy is indeed reasonable in vacuo. -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.
[gmx-users] Positive Potential Energy.
Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation. I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE. I have tried gromos ff and opsla ff. Both do this. A colleague of mine also gets this with his simulations although he reports negative potential when solvated. Any help would be appreciated or any explanation on how to interpret gromacs output on this. I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system. Daniel Sponseller PhD student George Mason University -- 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 potential energy during Energy minimization step
On 8/8/14, 7:25 AM, neha bharti wrote: I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. After Adding Ion genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL I preform energy minimization step. In energy minimization step I am getting possitive potential enargy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.1499341e+17 Maximum force =inf on atom 3300 Norm of force = 5.4206209e+18 its mention in the tutorial verify that the values of Epot and Fmax are reasonable before continuing I am trying alot but not able to fix the issue. Its mention in tutorial but I am not able to find the exactly what to do. You have infinite force, so you have unresolvable atomic clashes. -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.
[gmx-users] Positive potential energy during Energy minimization step
I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. After Adding Ion genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL I preform energy minimization step. In energy minimization step I am getting possitive potential enargy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.1499341e+17 Maximum force =inf on atom 3300 Norm of force = 5.4206209e+18 its mention in the tutorial verify that the values of Epot and Fmax are reasonable before continuing I am trying alot but not able to fix the issue. Its mention in tutorial but I am not able to find the exactly what to do. please help. With Regards Neha bharty -- 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.