[gmx-users] Energies in simulation and rerun using different core counts
Dear All, I've been having some issues with energies with gromacs running on various core counts for a 7469 polymer in solvent system, constraining all bonds and running with a 2fs time step. I used PME-shift (1.05nm, 1.10nm), and a shift with the same parameters for the VdW, I am using the OPLS-AA force field with fourierspacing = 0.10. and the md-vv integrator. I am running gromacs 4.5.5 compiled from the tarball on gromacs.org To try and track it down I ran a 100ps NVE simulation outputting coordinates and velocities every 1ps. I then used the trr trajectory file and ran: $ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 8_cores -reprod -nt 8 $ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 4_cores -reprod -nt 4 $ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 1_cores -reprod -nt 1 then: $ g_energy_d -f 8_cores.edr -o 8_cores.xvg << EOF 10 11 12 13 14 15 EOF etc. Where nve_short.tpr is the input file used for the original simulation and reference.trr is the trajectory it produced (I did not output forces into this which was an oversight). These were run on my machine a quad core hyper-threaded intel xeon. I also used performed the rerun on our local cluster on 12, 24, and 36 cores (dual 6 core intel xeon nodes with infiniband interconnects) The resulting energy files are significantly different energies for these snapshots summarised in this table: number of cores, Potential Energy,Standard Deviation reference 7912.74479607 180.525445863 1_cores9635.92644669 180.525445891 4_cores1061.8467459 244.14154375 8_cores 776.470114871 208.368028756 12_cores374.243502525 204.012539953 24_cores667.44876102 502.041766722 36_cores616.93105205 476.190500738 (reference is the energy extracted from the original simulation run on a 12 core node) The large variation in standard deviation means that these energies are not simply shifted but behaving differently which is apparent from a plot of the potential energies. has anyone else noticed any sort of inconsistency? Does anyone have any advice about what might cause this? Am I doing anything stupid? Thanks, Richard -- 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] Energies in simulation
Well, I tried to equilibrate the system, and I think the program has
included all the distortion that the system had been through. When I checked
the trajectory, the box was highly distorted as the simulation started, then
returned to its cubic shape. Also, I am a bit confused by the word
"strange". Well, based on manual the rvdw>rlist and it is. Also, authors in
the paper have tested U with various cutoff radii from 8-11A. The results
were very close! To make sure we are on the same page, the paper address is
J. Chem. Phys., Vol118, No.16 pp7401 (2003).
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:58 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> Well, when I set the box, I used 'editconf' command to rescale the box to
> have the right density which was ~997. After simulation, I got the
> following:
>
> Energy Average RMSD Fluct. Drift
> Tot-Drift
>
> ---
> Density (SI)956.765150.266130.596 0.257477
> 257.477
The RMSD is very large. Are you sure this is in equilibrium? It could be
that your box is exploding. Please check as well that the strange twin
range cut-off that you are using is what the original authors used.
>
>
>
> Payman
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of David van der Spoel
> Sent: June 8, 2009 11:29 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Energies in simulation
>
> Payman Pirzadeh wrote:
>> Here is the content of .itp file which I developed:
>>
>> ; This is an itp file to describe water's six-site model by H. Nada and
> J.P.
>> J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> and
>> 3 Coulomb sites
>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> 111.00
>> degrees, O-M and O-L are about 0.230A and 0.8892A respectively
>>
>> [ defaults ]
>> ; non-bondedtypecombrulegenpairsFudgeLJ
>> FudgeQQ N
>> 1 2 NO
>>
>> [ atomtypes ]
>> ;name masscharge ptype c6 c12
>> OW 15.9994 0.0 A 0.3115 0.714845562
>> HW 1.00800 0.477 A 0.0673 0.11541
>> MW 0.000 -0.866 D 0.000.00
>> LW 0.00-0.044 D 0.000.00
>>
>> [ moleculetype ]
>> ;molnamenrexcl
>> SOL 1
>>
>> [ atoms ]
>> ; nratomtyperesnr residuename atomcgnrcharge
>> 1 OW 1 SOL OW 1 0.0
>> 2 HW 1 SOL HW1 1 0.477
>> 3 HW 1 SOL HW2 1 0.477
>> 4 MW 1 SOL MW 1 -0.866
>> 5 LW 1 SOL LP1 1 -0.044
>> 6 LW 1 SOL LP2 1 -0.044
>>
>> [ settles ]
>> ; OWfunctiondoh dhh
>> 1 1 0.0980 0.15856
>>
>> [ dummies3 ]
>> ; These set of parameters are for M site which can be easily calculated
>> using TIP4P calculations from tip4p.itp
>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
>> b*(r(i)-r(k))
>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
>> Remember that OM is in the same direction of OH bonds.
>> ; Remember this site is in the same plane of OH bonds; so, its function 1
>> ;
>> ; site fromfunctiona b
>> 4 1 2 3 1 0.199642536 0.199642536
>>
>> ; Now we define the position of L sites which can be obtained from
> tip5p.itp
>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j))
> +
>> b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> bonds,
>> a minus sign is added. This part is similar to M site.
>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> the
>> magnitude of vector product of OH bonds.
>> ; This sites are tetrahedral sites;
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Well, when I set the box, I used 'editconf' command to rescale the box to
have the right density which was ~997. After simulation, I got the
following:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Density (SI)956.765150.266130.596 0.257477
257.477
The RMSD is very large. Are you sure this is in equilibrium? It could be
that your box is exploding. Please check as well that the strange twin
range cut-off that you are using is what the original authors used.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and
J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j))
+
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; P
RE: [gmx-users] Energies in simulation
Well, when I set the box, I used 'editconf' command to rescale the box to
have the right density which was ~997. After simulation, I got the
following:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Density (SI)956.765150.266130.596 0.257477
257.477
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> Here is the content of .itp file which I developed:
>
> ; This is an itp file to describe water's six-site model by H. Nada and
J.P.
> J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and
> 3 Coulomb sites
> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00
> degrees, O-M and O-L are about 0.230A and 0.8892A respectively
>
> [ defaults ]
> ; non-bondedtypecombrulegenpairsFudgeLJ
> FudgeQQ N
> 1 2 NO
>
> [ atomtypes ]
> ;name masscharge ptype c6 c12
> OW 15.9994 0.0 A 0.3115 0.714845562
> HW 1.00800 0.477 A 0.0673 0.11541
> MW 0.000 -0.866 D 0.000.00
> LW 0.00-0.044 D 0.000.00
>
> [ moleculetype ]
> ;molnamenrexcl
> SOL 1
>
> [ atoms ]
> ; nratomtyperesnr residuename atomcgnrcharge
> 1 OW 1 SOL OW 1 0.0
> 2 HW 1 SOL HW1 1 0.477
> 3 HW 1 SOL HW2 1 0.477
> 4 MW 1 SOL MW 1 -0.866
> 5 LW 1 SOL LP1 1 -0.044
> 6 LW 1 SOL LP2 1 -0.044
>
> [ settles ]
> ; OWfunctiondoh dhh
> 1 1 0.0980 0.15856
>
> [ dummies3 ]
> ; These set of parameters are for M site which can be easily calculated
> using TIP4P calculations from tip4p.itp
> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> b*(r(i)-r(k))
> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> Remember that OM is in the same direction of OH bonds.
> ; Remember this site is in the same plane of OH bonds; so, its function 1
> ;
> ; site fromfunctiona b
> 4 1 2 3 1 0.199642536 0.199642536
>
> ; Now we define the position of L sites which can be obtained from
tip5p.itp
> ; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j))
+
> b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds,
> a minus sign is added. This part is similar to M site.
> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the
> magnitude of vector product of OH bonds.
> ; This sites are tetrahedral sites; so, its function 4
> ;
> ; site fromfunctiona b c
> 5 1 2 3 4 -0.437172388-0.437172388
> 8.022961206
> 6 1 2 3 4 -0.437172388-0.437172388
> -8.022961206
>
> [ exclusions ]
> 1 2 3 4 5 6
> 2 1 3 4 5 6
> 3 1 2 4 5 6
> 4 1 2 3 5 6
> 5 1 2 3 4 6
> 6 1 2 3 4 5
>
>
> And here is the mdp file which I used for the simulation run:
> cpp = cpp
> include = -I../top
> define =
>
> ; Run control
>
> integrator = md
> dt = 0.001 ;1 fs
> nsteps = 100 ;10 ns
> comm_mode= linear
> nstcomm = 1
>
> ;Output control
>
> nstxout = 5000
> nstlog = 5000
> nstenergy= 5000
> nstxtcout= 1000
> xtc_grps =
> energygrps =
>
> ; Neighbour Searching
>
> nstlist = 10
> ns_type = grid
> rlist= 0.9
>
> ; Electrostatistics
>
> coulombtype = PME
> rcoulomb = 0.9
> epsilon_r= 1
>
> ; Vdw
>
> vdwtype
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is 111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p= 1.0
compressibility = 5.5e-5
ref_p= 1.0
gen_vel = yes
The expected Potential energy is supposed to be around -41.5kJ/mol while my
potential is around -22.2kJ/mol. I calculated the energies by g_energy
command.
And do yo have the right density?
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
To the best of my knowledge no, but how can I check that?
A. read the original paper: is your topology correct? Are the simulation
parameters the same?
B. post the itp file here and mdp file and specify energy and expected
energy. How abou
RE: [gmx-users] Energies in simulation
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is 111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p= 1.0
compressibility = 5.5e-5
ref_p= 1.0
gen_vel = yes
The expected Potential energy is supposed to be around -41.5kJ/mol while my
potential is around -22.2kJ/mol. I calculated the energies by g_energy
command.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> To the best of my knowledge no, but how can I check that?
>
A. read the original paper: is your topology correct? Are the simulation
parameters the same?
B. post the itp file here and mdp file and specify energy and expected
energy. How about energy units?
>
> -Original Message-
> From:
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote: To the best of my knowledge no, but how can I check that? A. read the original paper: is your topology correct? Are the simulation parameters the same? B. post the itp file here and mdp file and specify energy and expected energy. How about energy units? -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
To the best of my knowledge no, but how can I check that? -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: > Hi, > > I am using my own water model which I developed its .itp file. When > simulation is done after 1ns and energy is kinetic and potential > energies are analyzed, the kinetic value is almost OK, but the potential > energy is almost half of the value reported in literature and another MD > code that I am currently using. I double-checked the parameters I gave > in the .itp with TIP4P and TIP5P to make sure everything is correct in > format and unit. But I can not figure out the problem. Any ideas? > Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? > > > Payman > > > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote: Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energies in simulation
Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
