Re: [gmx-users] positive potential energy

[David van der Spoel]

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

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No. I just answered a similar question.

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[gmx-users] positive potential energy

[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
-- 
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

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Re: [gmx-users] Positive potential energy

[Mahsa]

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
>> 

Re: [gmx-users] Positive potential energy

[Justin Lemkul]

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   = 

Re: [gmx-users] Positive potential energy

[Mahsa]

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   = 

Re: [gmx-users] Positive potential energy

[Mahsa]

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.
> >
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> 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
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> 

Re: [gmx-users] Positive potential energy

[Mark Abraham]

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.
>
-- 
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Positive potential energy

[Mahsa E]

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!

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Re: [gmx-users] positive potential energy

[Mark Abraham]

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


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[gmx-users] positive potential energy

[Emran Heshmati]

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?
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[gmx-users] Positive potential energy

[Emran Heshmati]

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
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[gmx-users] Positive potential energy

[Emran Heshmati]

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
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[gmx-users] Positive potential energy

[Emran Heshmati]

 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
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[gmx-users] Positive Potential Energy.

[Dan Sponseller]

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
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Re: [gmx-users] Positive Potential Energy.

[Justin Lemkul]

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

==
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Re: [gmx-users] Positive Potential Energy.

[Tsjerk Wassenaar]

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


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Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] Positive potential energy during Energy minimization step

[neha bharti]

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
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Re: [gmx-users] Positive potential energy during Energy minimization step

[Justin Lemkul]

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

==
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