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
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Re: [gmx-users] How can I check external electric field was applied?

[이연경]

Thank you Dan,

I used two graphene sheets with freeze and one sodium ion and one chloride ion 
are between them.
It also had same ‘gmx potential’ result when simulated without graphene sheets.
 
I’m now using Gromacs 5.1.4, using PME for Ewald summation with NVE ensemble 
for this test system.


After finishing electric field test, I’m going to use following MDP for my 
original system.

< md.mdp>
define = -DPOSRES_GRA  -DPOSRES_CNT

Coulombtype=PME

t_couple = berendsen
tc_grps = GRA CNT SOL NA CL
tau_t = 0.1 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300 300

p_couple = Parrinello-Rahman
pcoupletype = semiisotropic
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0

constraints = none
constraint-algorithm = Lincs

E_z = 1 1 0

There is no gmx grompp error with this mdp, I just wonder the applied external 
e field is 1V.
Thank you, Regards :)

YK Lee











-Original Message-
From: "Dan Gil"
To: , "이연경"
Cc:
Sent: 2018. 2. 24 AM 2:36:06
Subject: Re: [gmx-users] How can I check external electric field was applied?

Hi,

You guessed correctly - gmx potential only calculates the electric field and 
potential of the system. It does not take into account the applied field.

Are you using walls in your system? If so, are you using the 3DC correction 
along with PME for Ewald summation? If you answered yes to both of these 
question, you need to use Gromacs version 2016.4 and forwards - there has been 
an important bug fix.

As long as your gmx grompp didn't return any warning or errors, I would expect 
it to be valid. You can share your MDP file with us and that might help.

Dan




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[gmx-users] The PMF curve is asymmetric (However many results of membrane penetration are symmetric)

[ygdcn]

Hi all: 
 
I tried to use MD simulation to pull a drug across the POPC membrane and to 
calculate PMF. I obtained the PMF curve following the guide 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/)
 
I found the PMF curve increases as the penetration process proceeds. The PMF 
curve is asymmetric, it increases in the whole time. However many results of 
membrane penetration are symmetric, e.g. increase earlier and decrease lately 
(X=0 in the central) . How can I get the similar result? There are examples of 
this in the GROMACS manual (see, e.g. the diagram for the cylinder geometry in 
the case of layered systems), but it is too difficult for me to understand it. 
I also read the answer 
(https://www.researchgate.net/post/How_to_pull_a_solute_across_liquid-liquid_interface).
  I am sure that a drug and a membrane will come closer when I used the 
negative pull rate. But I have some doubts whether the drug can continue to 
move ahead and leave the membrane after it arrive at the central of membrane.

Best regards, 



Best regards, 
祝  安好
--
Guodong YE 
Ph.D,  Professor
Department of Pharmaceutical Chemistry
School of Pharmaceutical Sciences
Guangzhou Medical University
Address: Guangzhou Medical University (Panyu Campus) 
Xinzao Town, Panyu District, Guangzhou, China, 511436
--
叶国东，博士，教授
广州医科大学 药学院 化学教研室
广州市番禺区新造镇


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[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
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Re: [gmx-users] g_sans calculation

[João Henriques]

I understand your pain, and the same could be said about gmx saxs as well.
As Micholas said, CRYSON might be a good choice as far as implicit solvent
methods go. Please notice that CRYSON is closed source, but it is well
documented in the literature (it is basically a reimplementation of
CRYSOL*).

*Svergun, D., Barberato, C., & Koch, M. H. (1995). J. Appl. Crystallogr.,
28(6), 768-773

J


On Fri, Feb 23, 2018 at 9:14 PM, Udaya Dahal  wrote:

>  Dear Gromacs Users,
>
> I am calculating the g_sans in the simulation but I am not able to find how
> it is calculated. The help content is minimal. I am just wondering if
> anyone has looked into how it is calculated (any reference to algorithm?).
>
> Regards,
> --
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Re: [gmx-users] g_sans calculation

[Smith, Micholas D.]

>From what I understand very few people use the g_sans tool. One alternative is 
>to use CRYSON (if you are looking at biopolymers such as 
>proteins/dna/polysaccarides). Alternatively, SASSENA is also an option but it 
>has a lot of dependences. 

CRYSON: https://www.embl-hamburg.de/biosaxs/manuals/cryson.html

SASSENA: www.sassena.org (accessible through the internet-wayback machine at:   
https://web.archive.org/web/20170724080028/http://www.sassena.org/  )

nMoldyn: 
http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/nmoldyn_user_guide.pdf/view

Hope this helps


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Udaya Dahal 

Sent: Friday, February 23, 2018 3:14 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] g_sans calculation

 Dear Gromacs Users,

I am calculating the g_sans in the simulation but I am not able to find how
it is calculated. The help content is minimal. I am just wondering if
anyone has looked into how it is calculated (any reference to algorithm?).

Regards,
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[gmx-users] g_sans calculation

[Udaya Dahal]

 Dear Gromacs Users,

I am calculating the g_sans in the simulation but I am not able to find how
it is calculated. The help content is minimal. I am just wondering if
anyone has looked into how it is calculated (any reference to algorithm?).

Regards,
-- 
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Re: [gmx-users] Potential energy coming out to be zero but not negative

[Alex]

Noone knows if you can continue your equilibration with this result, but 
it has nothing to do with the sign of the total energy. In the case of 
biomolecular forcefields involving quadratic energy terms for bonded 
stuff, the sign of the total energy is meaningless. _Reduction_ in total 
energy on EM is a correct trend. Do consult the manual for the energy 
terms used in your forcefield.


Alex


On 2/23/2018 11:32 AM, SHYANTANI MAITI wrote:

Hello Sir,

When I go for energy minimization for a protein complex containing 3
proteins, I obtain potential energy being minimized upto zero from
positive. The potential energy is not becoming negative even after running
for many steps as viewed in potential.xvg obtained after energy
minimzation.

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06
(kJ/mol)

Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy  obtained after
minimization need to be  negative in all cases? Can I continue my
equilibration with this result?

Thanking you



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[gmx-users] Potential energy coming out to be zero but not negative

[SHYANTANI MAITI]

Hello Sir,

When I go for energy minimization for a protein complex containing 3
proteins, I obtain potential energy being minimized upto zero from
positive. The potential energy is not becoming negative even after running
for many steps as viewed in potential.xvg obtained after energy
minimzation.

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06
(kJ/mol)

Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy  obtained after
minimization need to be  negative in all cases? Can I continue my
equilibration with this result?

Thanking you

-- 
Best regards,
*Shyantani Maiti*
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Re: [gmx-users] antigen-antibody insilico MD using GROMACS

[Raman Preet Singh]

Deepak:

Ag-Ab interactions occur via the hypervariable regions of the Ab. So the target 
amino acids for interaction will be much smaller. There are ample of docking 
softwares that can do this but that is a tricky affair at times. You may also 
look at protein-protein interaction softwares too.

Best

RPS

On Feb 23, 2018 9:45 PM, Krzysztof Makuch 
> wrote:
Hi,
If you don't know where exactly binding occurs you can't really do this
using only gromacs. I'd even suggest that until you have to, for antibodies
it might be better to stick mostly to docking software.
1 - you have to have antibody and antigen parametrized using the same
forcefield (FF).
2 - check stability in selected FF. Some make proteins more stable, other
less. It is important to pay attention if your protein really have to be
stable - for example if you take only part of the antibody it may not be
stable either under physiological or in silico conditions. That's why you
may have to use some restrains. Or you may not, you have to decide.
3 - you have to dock antigen in antibody using docking software (there are
many...). Above 50% of results will be ridiculous, often the best energy
still means stupid docking result.
In many cases you may stop here, just use multiple docking engines, compare
and you have supplementary materials for your molecular biology paper. If
you are really stubborn and you have ligand parametrized:
4 - restrain both molecules, equilibrate
5 - turn off restrains and check if your complex is stable. For antibodies
there is quite big chance that it won't be because:
- Ab. is dynamic structure which may change shape after binding and docking
can't simulate this
- Water competes for H-bonds and nobody can guarantee that your complex is
stable enough
- you may have wrong var region.
- the position of antigen may be slightly wrong and in result - break off
7. If everything is ok you can begin energy analysis - umbrella, FEP
In general I advice against being stubborn until this is your primary
project. Antibodies are nasty, little guys.
Best,
KM

2018-02-23 15:24 GMT+01:00 Deep kumar 
>:

> Hi Gromacs users,
>
> I am studying antigen-antibody interaction at protein level. I have a
> protein sequence (no crystal structure, length 180 residues) of the
> antigen, and have predicted the secondary structure of it (and modeled). By
> performing conserved domain search using inferno and NCBI I found out a
> domain in the antigen - PCC1 (residue 90 to 160). I am interested to know
> how the antigen interacts with the antibody (2000 residues) *in silico*.
> The ultimate aim is to find out "how the antigen interacts with the
> antibody, and predict the possible domains used by the antigen to interact
> with the antibody". I would really appreciate your valuable suggestions on
> how this can be done using GROMACS MD. Please let me know if I need to
> provide any further information. Thanks for your time.
>
> Regards,
> DK
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Re: [gmx-users] Minimum compute compatibility

[Mahmood Naderan]

I wrongly downloaded the v5.0. It seems that 2018 version is better! Such error 
is now solved.


Regards,
Mahmood 

On Friday, February 23, 2018, 4:10:15 PM GMT+3:30, Mahmood Naderan 
 wrote:  
 
 Hi,While I set -DGMX_GPU=on for a M2000 card, the make returned an error which 
says compute_20 is not supported. So, where in the options I can drop the 
compute_20 capability?

Regards,
Mahmood  
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Re: [gmx-users] How can I check external electric field was applied?

[Dan Gil]

Hi,

You guessed correctly - gmx potential only calculates the electric field
and potential of the system. It does not take into account the applied
field.

Are you using walls in your system? If so, are you using the 3DC correction
along with PME for Ewald summation? If you answered yes to both of these
question, you need to use Gromacs version 2016.4 and forwards - there has
been an important bug fix.

As long as your gmx grompp didn't return any warning or errors, I would
expect it to be valid. You can share your MDP file with us and that might
help.

Dan

On Fri, Feb 23, 2018 at 11:45 AM, 이연경  wrote:

>
> Dear Gromacs users,
>
> I’m testing a simple system that has one sodium ion and one chloide ion to
> check external electric field.
> ( Apply strong field along z axis, so I added the line of E_z = 1 10 0 to
> .mdp file. )
>
> After a short simulation, I used ‘gmx potential’ to check the field.
>
> But the result graphs of potential.xvg and field.xvg were different from
> my expectation.
>
> Although I applied 10v/nm along z axis, the electrostatic potential and
> electric field was not around 10V.
>
> Does ‘gmx potential’ calculate electric field and electrostatic potential
> including external force I applied, or just a system’s?
>
> If ‘gmx potential’ does not calculate including external forces, is there
> any method to check external field was correctly applied?
>
> Thanks for your time :)
>
>  YK Lee
>
>
>
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[gmx-users] How can I check external electric field was applied?

[이연경]

Dear Gromacs users,

I’m testing a simple system that has one sodium ion and one chloide ion to 
check external electric field.
( Apply strong field along z axis, so I added the line of E_z = 1 10 0 to .mdp 
file. )

After a short simulation, I used ‘gmx potential’ to check the field.

But the result graphs of potential.xvg and field.xvg were different from my 
expectation.

Although I applied 10v/nm along z axis, the electrostatic potential and 
electric field was not around 10V.

Does ‘gmx potential’ calculate electric field and electrostatic potential 
including external force I applied, or just a system’s?

If ‘gmx potential’ does not calculate including external forces, is there any 
method to check external field was correctly applied?

Thanks for your time :)

 YK Lee



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Re: [gmx-users] antigen-antibody insilico MD using GROMACS

[Krzysztof Makuch]

Hi,
If you don't know where exactly binding occurs you can't really do this
using only gromacs. I'd even suggest that until you have to, for antibodies
it might be better to stick mostly to docking software.
1 - you have to have antibody and antigen parametrized using the same
forcefield (FF).
2 - check stability in selected FF. Some make proteins more stable, other
less. It is important to pay attention if your protein really have to be
stable - for example if you take only part of the antibody it may not be
stable either under physiological or in silico conditions. That's why you
may have to use some restrains. Or you may not, you have to decide.
3 - you have to dock antigen in antibody using docking software (there are
many...). Above 50% of results will be ridiculous, often the best energy
still means stupid docking result.
In many cases you may stop here, just use multiple docking engines, compare
and you have supplementary materials for your molecular biology paper. If
you are really stubborn and you have ligand parametrized:
4 - restrain both molecules, equilibrate
5 - turn off restrains and check if your complex is stable. For antibodies
there is quite big chance that it won't be because:
- Ab. is dynamic structure which may change shape after binding and docking
can't simulate this
- Water competes for H-bonds and nobody can guarantee that your complex is
stable enough
- you may have wrong var region.
- the position of antigen may be slightly wrong and in result - break off
7. If everything is ok you can begin energy analysis - umbrella, FEP
In general I advice against being stubborn until this is your primary
project. Antibodies are nasty, little guys.
Best,
KM

2018-02-23 15:24 GMT+01:00 Deep kumar :

> Hi Gromacs users,
>
> I am studying antigen-antibody interaction at protein level. I have a
> protein sequence (no crystal structure, length 180 residues) of the
> antigen, and have predicted the secondary structure of it (and modeled). By
> performing conserved domain search using inferno and NCBI I found out a
> domain in the antigen - PCC1 (residue 90 to 160). I am interested to know
> how the antigen interacts with the antibody (2000 residues) *in silico*.
> The ultimate aim is to find out "how the antigen interacts with the
> antibody, and predict the possible domains used by the antigen to interact
> with the antibody". I would really appreciate your valuable suggestions on
> how this can be done using GROMACS MD. Please let me know if I need to
> provide any further information. Thanks for your time.
>
> Regards,
> DK
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[gmx-users] antigen-antibody insilico MD using GROMACS

[Deep kumar]

Hi Gromacs users,

I am studying antigen-antibody interaction at protein level. I have a
protein sequence (no crystal structure, length 180 residues) of the
antigen, and have predicted the secondary structure of it (and modeled). By
performing conserved domain search using inferno and NCBI I found out a
domain in the antigen - PCC1 (residue 90 to 160). I am interested to know
how the antigen interacts with the antibody (2000 residues) *in silico*.
The ultimate aim is to find out "how the antigen interacts with the
antibody, and predict the possible domains used by the antigen to interact
with the antibody". I would really appreciate your valuable suggestions on
how this can be done using GROMACS MD. Please let me know if I need to
provide any further information. Thanks for your time.

Regards,
DK
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[gmx-users] Minimum compute compatibility

[Mahmood Naderan]

Hi,While I set -DGMX_GPU=on for a M2000 card, the make returned an error which 
says compute_20 is not supported. So, where in the options I can drop the 
compute_20 capability?

Regards,
Mahmood
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