Hello Kiriko,
I’ve performed exactly those simulations for a multi-heme named OmcS up to 340 K (but only published the 270 and 300 K results: https://pubs.acs.org/doi/full/10.1021/acs.jpcb.2c06822). I never saw this issue, but to Claro’s point, I only ran briefly on CPUs to equilibrate the density; everything else was on GPUs.
Spikes in temperature cause me to think of spikes in velocities. I would be curious to know how you are building the topology with TLEaP? Are the necessary bonds between the heme and the protein explicitly defined (as they must be)?
I’ve developed a program to, among other tasks, automatically prepare multi-heme proteins for AMBER simulations. Maybe it can be of use to you. The GitHub repo is here: https://github.com/Mag14011/BioDC.git
Best regards,
Matthew
On Jan 6, 2025, at 12:13 PM, Kiriko Terai via AMBER <amber.ambermd.org> wrote:
Hello,
I have recently been attempting to simulate a multi-heme protein system in explicit solvent OPC at temperatures 275, 300, 325, 350, and 375 K. I have prepared .prmtop and .inpcrd files. I am currently going through minimization and relaxation steps following the protocol here: https://ambermd.org/tutorials/basic/tutorial13/index.php#Files_
I can minimize my system, heat the system from 100 K up to the target temperature, run constrained NVT/NPT equilibration, and relax the system by gradually decreasing the restraints. But when I check the relaxation using cpptraj and analyze the temperature, density, volume, and etc., I find obvious temperature spikes in the Temperature.agr plot. I do not see any issues with Density.agr and Volume.agr.
To fix this issue, I have tried running the relaxation for longer times, running the 2mdheat.in step with smaller time steps (1fs vs 0.5fs), and running the relaxation steps with more gradual decrease of restraint_wt. In the manual, restraint_wt changes from 100, 10, 0.1 and to 0. Instead, I changed from 100, 50, 10, 0.1 and to 0. However, the temperature spikes are still present.
Any help would be much appreciated. Below are my input files for the minimization and relaxation steps for target temperature 375K. I also attach the Temperature.agr that shows the temperature spikes.
Thank you,
Kiriko
[cid:image001.png.01DB6032.56E06760]
1min.in:
minimization of solvent
&cntrl
imin = 1, maxcyc = 10000,
ncyc = 10000, ntx = 1,
ntwe = 0, ntwr = 500, ntpr = 50,
ntc = 2, ntf = 2, ntb = 1, ntp = 0,
cut = 10.0,
ntr=1, restraintmask = ':1-81',
restraint_wt = 100.,
ioutfm=1, ntxo=2,
/
2mdheat.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 0, ntx = 1, ig = -1,
tempi = 100.0, temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1., ntb = 1, ntp = 0,
nscm = 0,
ntr=1, restraintmask=':1-81', restraint_wt=100.0
nmropt=1,
ioutfm=1, ntxo=2,
/
&wt TYPE="TEMP0", istep1=0, istep2=1000000, value1=100., value2=375., /
&wt TYPE="END", /
3md.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1, barostat = 2,
nscm = 0,
ntr=1, restraintmask=':1-81', restraint_wt=100.
ioutfm=1, ntxo=2,
/
4md.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
nscm = 0, barostat = 2,
ntr=1, restraintmask=':1-81', restraint_wt=10.
ioutfm=1, ntxo=2,
/
5min.in:
Minimization of everything excluding backbone
&cntrl
imin = 1, maxcyc = 10000,
ncyc = 5000, ntx = 1,
ntwe = 0, ntwr = 500, ntpr = 50,
ntc = 2, ntf = 2, ntb = 1, ntp = 0,
cut = 8.0,
ntr=1, restraintmask="@CA,N,C", restraint_wt=10.
ioutfm=1, ntxo=2,
/
6md.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 0, ntx = 1, ig = -1,
tempi = 375.0, temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
nscm = 0, barostat = 2,
ntr=1, restraintmask=".CA,N,C", restraint_wt=10.
ioutfm=1, ntxo=2,
/
7md.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
nscm = 0, barostat = 2,
ntr=1, restraintmask="@CA,N,C", restraint_wt=1.
ioutfm=1, ntxo=2,
/
8md.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
nscm = 0, barostat = 2,
ntr=1, restraintmask=".CA,N,C", restraint_wt=0.1
ioutfm=1, ntxo=2,
/
9md.in:
&cntrl
imin = 0, nstlim = 1000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
temp0 = 375.0,
ntc = 2, ntf = 2, tol = 0.00001,
ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 8.0, iwrap = 0,
ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
nscm = 1000, barostat = 2,
ioutfm=1, ntxo=2,
/
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Received on Mon Jan 06 2025 - 10:00:02 PST
