- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Zhiyi Wu <zhiyi.wu.msdtc.ox.ac.uk>

Date: Sat, 11 May 2019 21:10:13 +0000

Dear Amber user,

I was trying to run an explicit solvent cpHMD simulation on a membrane protein system with amber18. After equilibrating the system in NVT ensemble for 200ps, I tried to move the system to NPT ensemble with MC barostat. However, MC barostat will cause the system to stuck indefinitely (~12 hours) in the first step but Berendsen will keep the system going normally.

MC barostat do work properly in non-MPI mode in a local machine on CPU. After equilibrating with MC barostat for 200ps, the system has been moved to the cluster to run in MPI mode again in a 16 core CPU node but it still stuck indefinitely, where the last few lines of the output file is:

4. RESULTS

--------------------------------------------------------------------------------

---------------------------------------------------

APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION

using 5000.0 points per unit in tabled values

TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff

| CHECK switch(x): max rel err = 0.3316E-14 at 2.351880

| CHECK d/dx switch(x): max rel err = 0.8066E-11 at 2.747240

---------------------------------------------------

|---------------------------------------------------

| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION

| with 50.0 points per unit in tabled values

| Relative Error Limit not exceeded for r .gt. 2.34

| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION

| with 50.0 points per unit in tabled values

| Relative Error Limit not exceeded for r .gt. 2.81

|---------------------------------------------------

| MC Barostat: Decreasing size of volume moves

| MC Barostat: Decreasing size of volume moves

The input file is:

Relax in NPT

&cntrl

imin = 0, ! No minimization.

ig = -1, ! pseudo-random number generator

ntx = 5, ! Coordinates and velocities will be read

irest = 1, ! Restart the simulation

ntpr = 2500, ! Frequency of printing of the energy and its components.

ntwx = 2500, ! Every ntwx steps, the coordinates will be written to the mdcrd file.

ntwr = 10000,! Every ntwr steps during dynamics, the “restrt” file will be written.

ntf = 2,

ntc = 2, ! bonds involving hydrogen are constrained

ntb = 2, ! constant pressure

ntp = 2, ! 1:isotropic, 2:anisotropic, 3:semiisotropic

barostat = 2, ! Monte Carlo barostat

mcbarint = 50, ! Number of steps between the Monte Carlo barostat

pres0 = 1.0, ! Reference pressure

cut = 10.0, ! Non-bond cut off

nstlim = 2500000,! Perform MD for 500,000 steps = 1 ns

nscm = 1250, ! removal of COM

dt = 0.002, ! timestep

tempi = 300.0, ! Initial temperature.

temp0 = 300.0, ! Reference temperature at which the system is to be kept,

ntt = 3, ! Langevin dynamics

gamma_ln = 2.0, ! Collision frequency

ntr = 1, ! position restraint

restraintmask = '(:1-207)&(!.H=)',

restraint_wt = 25.0, !The weight (in kcal/mol−Å^2) for the positional restraints.

icnstph=2 ! cpHMD in explicit solvent

ntcnstph=100 ! Attempt protonation every 100 steps

ntrelax=100 ! 200 fs relaxed solvent distribution

solvph=7.0 ! pH of the Golgi pH

saltcon=0.1 ! Physiological salt concentration

/

Kind regards,

Zhiyi Wu

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat May 11 2019 - 14:30:02 PDT

Date: Sat, 11 May 2019 21:10:13 +0000

Dear Amber user,

I was trying to run an explicit solvent cpHMD simulation on a membrane protein system with amber18. After equilibrating the system in NVT ensemble for 200ps, I tried to move the system to NPT ensemble with MC barostat. However, MC barostat will cause the system to stuck indefinitely (~12 hours) in the first step but Berendsen will keep the system going normally.

MC barostat do work properly in non-MPI mode in a local machine on CPU. After equilibrating with MC barostat for 200ps, the system has been moved to the cluster to run in MPI mode again in a 16 core CPU node but it still stuck indefinitely, where the last few lines of the output file is:

4. RESULTS

--------------------------------------------------------------------------------

---------------------------------------------------

APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION

using 5000.0 points per unit in tabled values

TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff

| CHECK switch(x): max rel err = 0.3316E-14 at 2.351880

| CHECK d/dx switch(x): max rel err = 0.8066E-11 at 2.747240

---------------------------------------------------

|---------------------------------------------------

| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION

| with 50.0 points per unit in tabled values

| Relative Error Limit not exceeded for r .gt. 2.34

| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION

| with 50.0 points per unit in tabled values

| Relative Error Limit not exceeded for r .gt. 2.81

|---------------------------------------------------

| MC Barostat: Decreasing size of volume moves

| MC Barostat: Decreasing size of volume moves

The input file is:

Relax in NPT

&cntrl

imin = 0, ! No minimization.

ig = -1, ! pseudo-random number generator

ntx = 5, ! Coordinates and velocities will be read

irest = 1, ! Restart the simulation

ntpr = 2500, ! Frequency of printing of the energy and its components.

ntwx = 2500, ! Every ntwx steps, the coordinates will be written to the mdcrd file.

ntwr = 10000,! Every ntwr steps during dynamics, the “restrt” file will be written.

ntf = 2,

ntc = 2, ! bonds involving hydrogen are constrained

ntb = 2, ! constant pressure

ntp = 2, ! 1:isotropic, 2:anisotropic, 3:semiisotropic

barostat = 2, ! Monte Carlo barostat

mcbarint = 50, ! Number of steps between the Monte Carlo barostat

pres0 = 1.0, ! Reference pressure

cut = 10.0, ! Non-bond cut off

nstlim = 2500000,! Perform MD for 500,000 steps = 1 ns

nscm = 1250, ! removal of COM

dt = 0.002, ! timestep

tempi = 300.0, ! Initial temperature.

temp0 = 300.0, ! Reference temperature at which the system is to be kept,

ntt = 3, ! Langevin dynamics

gamma_ln = 2.0, ! Collision frequency

ntr = 1, ! position restraint

restraintmask = '(:1-207)&(!.H=)',

restraint_wt = 25.0, !The weight (in kcal/mol−Å^2) for the positional restraints.

icnstph=2 ! cpHMD in explicit solvent

ntcnstph=100 ! Attempt protonation every 100 steps

ntrelax=100 ! 200 fs relaxed solvent distribution

solvph=7.0 ! pH of the Golgi pH

saltcon=0.1 ! Physiological salt concentration

/

Kind regards,

Zhiyi Wu

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Sat May 11 2019 - 14:30:02 PDT

Custom Search