Re: [gmx-users] Running MD simulations at a particular temperature
On 10/25/17 9:33 AM, Dilip H N wrote: Sir, As u have mentioned in the link http://www.gromacs.org/Documen tation/Terminology/Force_Fields/CHARMM the cutoffs are described here for CHARMM FF. So similarly, how can i get the cutoffs for OPLSAA, Amber, GROMOS etc., forcefields in gromacs..?? Is there any source, or only through literature survey the cutoffs need to be fixed..?? Read the literature. You shouldn't be using a force field if you don't know how it works, what it's good for and what it fails at, and what the best practices are. -Justin Thank you.. <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_medium=signature_campaign=signaturevirality> <#> On Wed, Oct 18, 2017 at 7:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 10/18/17 9:41 AM, Dilip H N wrote: Justin Sir, Even i am also using Charmm 36FF. So as u have mentioned in previois message, can u kindly suggest then what ate the correct cutoffs..?? And what would be the other modifications that needs to be done in order to incorporate the Charmm FF I think I post this link to the mailing list weekly... http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -Justin Thank you <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gma il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail& utm_medium=signature_campaign=signaturevirality> On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 10/18/17 9:14 AM, Pandya, Akash wrote: So I equilibrated my system at 338.15 K , do I still need to use the simulated annealing option to maintain that temperature? My NPT mdp file is shown below. Simply maintaining a temperature is done by employing a thermostat and reference temperature. Annealing is used to change temperature over time, so you don't need that here. title = CHARMM27 A33FabGLY NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) Your title says CHARMM, but these aren't the correct cutoffs for using the CHARMM force field. -Justin ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 338.15338.15 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 17 October 2017 10:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature Hi, That's your question as part of your experimental design. Why do you want to do simulated annealing? Mark On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash < akash.pandya...@ucl.ac.uk
Re: [gmx-users] Running MD simulations at a particular temperature
Sir, As u have mentioned in the link http://www.gromacs.org/Documen tation/Terminology/Force_Fields/CHARMM the cutoffs are described here for CHARMM FF. So similarly, how can i get the cutoffs for OPLSAA, Amber, GROMOS etc., forcefields in gromacs..?? Is there any source, or only through literature survey the cutoffs need to be fixed..?? Thank you.. <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_medium=signature_campaign=signaturevirality> <#> On Wed, Oct 18, 2017 at 7:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/18/17 9:41 AM, Dilip H N wrote: > >> Justin Sir, >> Even i am also using Charmm 36FF. So as u have mentioned in previois >> message, can u kindly suggest then what ate the correct cutoffs..?? >> And what would be the other modifications that needs to be done in order >> to >> incorporate the Charmm FF >> > > I think I post this link to the mailing list weekly... > > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM > > -Justin > > Thank you >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> <https://chrome.google.com/webstore/detail/mailtrack-for-gma >> il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail& >> utm_medium=signature_campaign=signaturevirality> >> >> >> On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 10/18/17 9:14 AM, Pandya, Akash wrote: >>> >>> So I equilibrated my system at 338.15 K , do I still need to use the >>>> simulated annealing option to maintain that temperature? My NPT mdp >>>> file is >>>> shown below. >>>> >>>> Simply maintaining a temperature is done by employing a thermostat and >>> reference temperature. Annealing is used to change temperature over time, >>> so you don't need that here. >>> >>> title = CHARMM27 A33FabGLY NPT equilibration >>> >>>> define = -DPOSRES ; position restrain the protein >>>> ; Run parameters >>>> integrator = md; leap-frog integrator >>>> nsteps = 5 ; 2 * 5 = 100 ps >>>> dt = 0.002 ; 2 fs >>>> ; Output control >>>> nstxout = 100 ; save coordinates every 0.2 ps >>>> nstvout = 100 ; save velocities every 0.2 ps >>>> nstenergy = 100 ; save energies every 0.2 ps >>>> nstlog = 100 ; update log file every 0.2 ps >>>> ; Bond parameters >>>> continuation= yes ; Restarting after NVT >>>> constraint_algorithm = lincs; holonomic constraints >>>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >>>> constrained >>>> lincs_iter = 1 ; accuracy of LINCS >>>> lincs_order = 4 ; also related to accuracy >>>> ; Neighborsearching >>>> ns_type = grid ; search neighboring grid cells >>>> nstlist = 5 ; 10 fs >>>> rlist = 1.0 ; short-range neighborlist cutoff (in >>>> nm) >>>> rcoulomb= 1.0 ; short-range electrostatic cutoff (in >>>> nm) >>>> rvdw= 1.0 ; short-range van der Waals cutoff (in >>>> nm) >>>> >>>> Your title says CHARMM, but these aren't the correct cutoffs for using >>> the >>> CHARMM force field. >>> >>> -Justin >>> >>> >>> ; Electrostatics >>> >>>> coulombtype = PME ; Particle Mesh Ewald for long-range >>>> electrostatics >>>> pme_order = 4 ; cubic interpolation >>>> fourierspacing = 0.16 ; grid spacing for FFT >>>> ; Temperature coupling is on >>>> tcoupl = Nose-Hoover ; Nose-Hoover thermostat >>>> tc-grps = Protein Non-Protein ; two coupling groups - more >>>> accurate >>>> tau_t = 0.5 0.5 ; time constant, in ps >>>> ref_t = 338.15338.15 ; reference temperature, one for >>>> each group, in K >>>> ; Pressure coupling is on >>>> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT >>>> pcoupltype = isotropic
Re: [gmx-users] Running MD simulations at a particular temperature
On 10/18/17 9:41 AM, Dilip H N wrote: Justin Sir, Even i am also using Charmm 36FF. So as u have mentioned in previois message, can u kindly suggest then what ate the correct cutoffs..?? And what would be the other modifications that needs to be done in order to incorporate the Charmm FF I think I post this link to the mailing list weekly... http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -Justin Thank you <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_medium=signature_campaign=signaturevirality> On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 10/18/17 9:14 AM, Pandya, Akash wrote: So I equilibrated my system at 338.15 K , do I still need to use the simulated annealing option to maintain that temperature? My NPT mdp file is shown below. Simply maintaining a temperature is done by employing a thermostat and reference temperature. Annealing is used to change temperature over time, so you don't need that here. title = CHARMM27 A33FabGLY NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) Your title says CHARMM, but these aren't the correct cutoffs for using the CHARMM force field. -Justin ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 338.15338.15 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 17 October 2017 10:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature Hi, That's your question as part of your experimental design. Why do you want to do simulated annealing? Mark On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya...@ucl.ac.uk wrote: Is simulated annealing carried out during NPT or in the production run? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 20 September 2017 03:20 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature On 9/19/17 4:25 PM, Pandya, Akash wrote: Hi all, I want to run my MD simulation at 65 degrees Celsius. The mdp file has a field as shown below: ref_t= 338.15 338.15 ; reference temperature, one for each group, in K I am wondering whether the simulation has already reached the desired temperature or does it heat up to 65 degrees throughout the course of the simulation? I hope this makes sense. The answer depends on what you're doing. If you've set &qu
Re: [gmx-users] Running MD simulations at a particular temperature
Justin Sir, Even i am also using Charmm 36FF. So as u have mentioned in previois message, can u kindly suggest then what ate the correct cutoffs..?? And what would be the other modifications that needs to be done in order to incorporate the Charmm FF Thank you <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_medium=signature_campaign=signaturevirality> On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/18/17 9:14 AM, Pandya, Akash wrote: > >> So I equilibrated my system at 338.15 K , do I still need to use the >> simulated annealing option to maintain that temperature? My NPT mdp file is >> shown below. >> > > Simply maintaining a temperature is done by employing a thermostat and > reference temperature. Annealing is used to change temperature over time, > so you don't need that here. > > title = CHARMM27 A33FabGLY NPT equilibration >> define = -DPOSRES ; position restrain the protein >> ; Run parameters >> integrator = md; leap-frog integrator >> nsteps = 5 ; 2 * 5 = 100 ps >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 100 ; save coordinates every 0.2 ps >> nstvout = 100 ; save velocities every 0.2 ps >> nstenergy = 100 ; save energies every 0.2 ps >> nstlog = 100 ; update log file every 0.2 ps >> ; Bond parameters >> continuation= yes ; Restarting after NVT >> constraint_algorithm = lincs; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >> constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> rlist = 1.0 ; short-range neighborlist cutoff (in nm) >> rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) >> rvdw= 1.0 ; short-range van der Waals cutoff (in nm) >> > > Your title says CHARMM, but these aren't the correct cutoffs for using the > CHARMM force field. > > -Justin > > > ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> ; Temperature coupling is on >> tcoupl = Nose-Hoover ; Nose-Hoover thermostat >> tc-grps = Protein Non-Protein ; two coupling groups - more >> accurate >> tau_t = 0.5 0.5 ; time constant, in ps >> ref_t = 338.15338.15 ; reference temperature, one for >> each group, in K >> ; Pressure coupling is on >> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT >> pcoupltype = isotropic ; uniform scaling of box vectors >> tau_p = 2.0 ; time constant, in ps >> ref_p = 1.0 ; reference pressure, in bar >> compressibility = 4.5e-5; isothermal compressibility of water, >> bar^-1 >> refcoord_scaling = com >> ; Periodic boundary conditions >> pbc = xyz ; 3-D PBC >> ; Dispersion correction >> DispCorr= EnerPres ; account for cut-off vdW scheme >> ; Velocity generation >> gen_vel = no; Velocity generation is off >> >> >> Akash >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark >> Abraham >> Sent: 17 October 2017 10:28 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Running MD simulations at a particular >> temperature >> >> Hi, >> >> That's your question as part of your experimental design. Why do you want >> to do simulated annealing? >> >> Mark >> >> On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya...@ucl.ac.uk >> > >> wrote: >> >> Is simulated annealing carried out during NPT or in the production run? >>> >>> Akash >>> >>> -Original Message- >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >>> gromacs.org_gmx-users-boun...@maillist
Re: [gmx-users] Running MD simulations at a particular temperature
On 10/18/17 9:14 AM, Pandya, Akash wrote: So I equilibrated my system at 338.15 K , do I still need to use the simulated annealing option to maintain that temperature? My NPT mdp file is shown below. Simply maintaining a temperature is done by employing a thermostat and reference temperature. Annealing is used to change temperature over time, so you don't need that here. title = CHARMM27 A33FabGLY NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) Your title says CHARMM, but these aren't the correct cutoffs for using the CHARMM force field. -Justin ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 338.15338.15 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 17 October 2017 10:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature Hi, That's your question as part of your experimental design. Why do you want to do simulated annealing? Mark On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: Is simulated annealing carried out during NPT or in the production run? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 20 September 2017 03:20 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature On 9/19/17 4:25 PM, Pandya, Akash wrote: Hi all, I want to run my MD simulation at 65 degrees Celsius. The mdp file has a field as shown below: ref_t= 338.15 338.15 ; reference temperature, one for each group, in K I am wondering whether the simulation has already reached the desired temperature or does it heat up to 65 degrees throughout the course of the simulation? I hope this makes sense. The answer depends on what you're doing. If you've set "gen-vel = yes" and "gen-temp = 338.15" then you are initializing a simulation with random velocities according to a Maxwell distribution at that temperature. If your system is at some other temperature and you're just trying to use a thermostat to force a change in that temperature, there's no real "warming" going on, rather the thermostat is going to push the velocity distribution towards the desired temperature. Warming a system is done via simulated annealing options. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540
Re: [gmx-users] Running MD simulations at a particular temperature
So I equilibrated my system at 338.15 K , do I still need to use the simulated annealing option to maintain that temperature? My NPT mdp file is shown below. title = CHARMM27 A33FabGLY NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 338.15338.15 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 17 October 2017 10:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature Hi, That's your question as part of your experimental design. Why do you want to do simulated annealing? Mark On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > Is simulated annealing carried out during NPT or in the production run? > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin > Lemkul > Sent: 20 September 2017 03:20 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Running MD simulations at a particular > temperature > > > > On 9/19/17 4:25 PM, Pandya, Akash wrote: > > Hi all, > > > > I want to run my MD simulation at 65 degrees Celsius. The mdp file > > has a > field as shown below: > > > > ref_t= 338.15 338.15 ; reference > temperature, one for each group, in K > > > > I am wondering whether the simulation has already reached the > > desired > temperature or does it heat up to 65 degrees throughout the course of > the simulation? I hope this makes sense. > > The answer depends on what you're doing. If you've set "gen-vel = yes" > and "gen-temp = 338.15" then you are initializing a simulation with > random velocities according to a Maxwell distribution at that > temperature. If your system is at some other temperature and you're > just trying to use a thermostat to force a change in that temperature, > there's no real "warming" > going on, rather the thermostat is going to push the velocity > distribution towards the desired temperature. Warming a system is > done via simulated annealing options. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://
Re: [gmx-users] Running MD simulations at a particular temperature
Hi, That's your question as part of your experimental design. Why do you want to do simulated annealing? Mark On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > Is simulated annealing carried out during NPT or in the production run? > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin > Lemkul > Sent: 20 September 2017 03:20 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Running MD simulations at a particular temperature > > > > On 9/19/17 4:25 PM, Pandya, Akash wrote: > > Hi all, > > > > I want to run my MD simulation at 65 degrees Celsius. The mdp file has a > field as shown below: > > > > ref_t= 338.15 338.15 ; reference > temperature, one for each group, in K > > > > I am wondering whether the simulation has already reached the desired > temperature or does it heat up to 65 degrees throughout the course of the > simulation? I hope this makes sense. > > The answer depends on what you're doing. If you've set "gen-vel = yes" > and "gen-temp = 338.15" then you are initializing a simulation with random > velocities according to a Maxwell distribution at that temperature. If your > system is at some other temperature and you're just trying to use a > thermostat to force a change in that temperature, there's no real "warming" > going on, rather the thermostat is going to push the velocity distribution > towards the desired temperature. Warming a system is done via simulated > annealing options. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Running MD simulations at a particular temperature
Is simulated annealing carried out during NPT or in the production run? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 20 September 2017 03:20 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature On 9/19/17 4:25 PM, Pandya, Akash wrote: > Hi all, > > I want to run my MD simulation at 65 degrees Celsius. The mdp file has a > field as shown below: > > ref_t= 338.15 338.15 ; reference > temperature, one for each group, in K > > I am wondering whether the simulation has already reached the desired > temperature or does it heat up to 65 degrees throughout the course of the > simulation? I hope this makes sense. The answer depends on what you're doing. If you've set "gen-vel = yes" and "gen-temp = 338.15" then you are initializing a simulation with random velocities according to a Maxwell distribution at that temperature. If your system is at some other temperature and you're just trying to use a thermostat to force a change in that temperature, there's no real "warming" going on, rather the thermostat is going to push the velocity distribution towards the desired temperature. Warming a system is done via simulated annealing options. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Running MD simulations at a particular temperature
On 9/19/17 4:25 PM, Pandya, Akash wrote: Hi all, I want to run my MD simulation at 65 degrees Celsius. The mdp file has a field as shown below: ref_t= 338.15 338.15 ; reference temperature, one for each group, in K I am wondering whether the simulation has already reached the desired temperature or does it heat up to 65 degrees throughout the course of the simulation? I hope this makes sense. The answer depends on what you're doing. If you've set "gen-vel = yes" and "gen-temp = 338.15" then you are initializing a simulation with random velocities according to a Maxwell distribution at that temperature. If your system is at some other temperature and you're just trying to use a thermostat to force a change in that temperature, there's no real "warming" going on, rather the thermostat is going to push the velocity distribution towards the desired temperature. Warming a system is done via simulated annealing options. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Running MD simulations at a particular temperature
Hi all, I want to run my MD simulation at 65 degrees Celsius. The mdp file has a field as shown below: ref_t= 338.15 338.15 ; reference temperature, one for each group, in K I am wondering whether the simulation has already reached the desired temperature or does it heat up to 65 degrees throughout the course of the simulation? I hope this makes sense. Many thanks, Akash -- 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.
