Re: [gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 1:55 AM, Alex  wrote:

> Hi,
>
> The answer is clearly in the error, just read it please:
> 2.848793 > 0.49 * (4/2) where 4 is the box length.
>
> You can either keep the “pull_coord1_geometry= distance” and increase
> the box length or change the “pull_coord1_geometry” to  “=
> direction-periodic“. I prefer the former though.
>
> Cheers,
> Alex
>
>> I've got it.
>
> would you please answer to another questions too? thank you in advance
>
>

>
>
> On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:
>
> > Hi;
> >
> > This is md_pull.mdp
> >
> > integrator   = md
> > dt   = 0.001
> > nsteps   = 200
> > nstxout  = 0
> > nstvout  = 0
> > nstfout  = 0
> > nstlog   = 500
> > nstenergy= 1000
> > nstxtcout= 1000
> > rlist= 1.5
> > rcoulomb = 1.5
> > rvdw = 1.2
> > coulombtype  = pme
> > cutoff-scheme= group
> > vdwtype  = Switch
> > rvdw_switch  = 1.0
> > pcoupl   = no
> > gen-vel  = yes
> > gen-temp = 0
> > gen-seed = 173529
> > constraints  = h-bonds
> > pbc  = xy
> > freezegrps   = WAL ZnS
> > freezedim= Y Y Y Y Y Y
> > energygrp-excl   = WAL WAL ZnS ZnS
> > energygrps   = SOL WAL ZnS Protein NA CL
> > nwall= 2
> > wall-atomtype= C C
> > wall-type= 9-3
> > wall-density = 150 150
> > wall-ewald-zfac  = 3
> > ewald-geometry   = 3dc
> > fourierspacing   = 0.12
> > tcoupl   = v-rescale
> > tc-grps  = System
> > tau-t= 0.1
> > ref-t= 300
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 1
> > pull_group1_name= ZnS
> > pull_group2_name= Protein
> > pull_coord1_type= umbrella
> > pull_coord1_geometry= distance
> > pull_coord1_groups  = 1 2
> > pull__coord1_dim= N N Y
> > pull_coord1_rate  = -0.001; 1 nm per  ns
> > pull_coord1_k = 5000
> > pull_coord1_start  = yes
> >
> > Program gmx grompp, VERSION 5.1.4
> >
> > Fatal error:
> > Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> > times the box size (2.00).
> > You might want to consider using "pull-geometry = direction-periodic"
> > instead.
> >
> > the box size is= 4 4 12
> >
> > could you please help me to resolve it?
> > -
> > Mr.Lemkul told me rcutt-off is wrong and
> >
> >  i should'nt put "cutoff-scheme= group" >>>but when i remove
> > it i'll get  this error too;
> >
> >   >>With Verlet lists rcoulomb!=rvdw is not supported
> >
> > i know it's wrong solution but what is my alternative?!!
> >
> > --
> > -dummy particle should move towards the surface with a constant speed of
> 1
> > nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> > corresponding to the spring constant of 5000.
> >
> > I DON'T know how should i implement deltaZ(=2)? which .mdp option refers
> to
> > it?!
> >
> > thank you so much
> >
> > Best regards
> > Rose
> > --
> > 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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> >
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Re: [gmx-users] umbrella sampling

[Alex]

Hi,

The answer is clearly in the error, just read it please:
2.848793 > 0.49 * (4/2) where 4 is the box length.

You can either keep the “pull_coord1_geometry= distance” and increase
the box length or change the “pull_coord1_geometry” to  “=
direction-periodic“. I prefer the former though.

Cheers,
Alex

On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:

> Hi;
>
> This is md_pull.mdp
>
> integrator   = md
> dt   = 0.001
> nsteps   = 200
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 500
> nstenergy= 1000
> nstxtcout= 1000
> rlist= 1.5
> rcoulomb = 1.5
> rvdw = 1.2
> coulombtype  = pme
> cutoff-scheme= group
> vdwtype  = Switch
> rvdw_switch  = 1.0
> pcoupl   = no
> gen-vel  = yes
> gen-temp = 0
> gen-seed = 173529
> constraints  = h-bonds
> pbc  = xy
> freezegrps   = WAL ZnS
> freezedim= Y Y Y Y Y Y
> energygrp-excl   = WAL WAL ZnS ZnS
> energygrps   = SOL WAL ZnS Protein NA CL
> nwall= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> pull= yes
> pull_ngroups= 2
> pull_ncoords= 1
> pull_group1_name= ZnS
> pull_group2_name= Protein
> pull_coord1_type= umbrella
> pull_coord1_geometry= distance
> pull_coord1_groups  = 1 2
> pull__coord1_dim= N N Y
> pull_coord1_rate  = -0.001; 1 nm per  ns
> pull_coord1_k = 5000
> pull_coord1_start  = yes
>
> Program gmx grompp, VERSION 5.1.4
>
> Fatal error:
> Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> times the box size (2.00).
> You might want to consider using "pull-geometry = direction-periodic"
> instead.
>
> the box size is= 4 4 12
>
> could you please help me to resolve it?
> -
> Mr.Lemkul told me rcutt-off is wrong and
>
>  i should'nt put "cutoff-scheme= group" >>>but when i remove
> it i'll get  this error too;
>
>   >>With Verlet lists rcoulomb!=rvdw is not supported
>
> i know it's wrong solution but what is my alternative?!!
>
> --
> -dummy particle should move towards the surface with a constant speed of 1
> nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> corresponding to the spring constant of 5000.
>
> I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
> it?!
>
> thank you so much
>
> Best regards
> Rose
> --
> 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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[gmx-users] umbrella sampling

[rose rahmani]

Hi;

This is md_pull.mdp

integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull__coord1_dim= N N Y
pull_coord1_rate  = -0.001; 1 nm per  ns
pull_coord1_k = 5000
pull_coord1_start  = yes

Program gmx grompp, VERSION 5.1.4

Fatal error:
Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
times the box size (2.00).
You might want to consider using "pull-geometry = direction-periodic"
instead.

the box size is= 4 4 12

could you please help me to resolve it?
-
Mr.Lemkul told me rcutt-off is wrong and

 i should'nt put "cutoff-scheme= group" >>>but when i remove
it i'll get  this error too;

  >>With Verlet lists rcoulomb!=rvdw is not supported

i know it's wrong solution but what is my alternative?!!

--
-dummy particle should move towards the surface with a constant speed of 1
nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
corresponding to the spring constant of 5000.

I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
it?!

thank you so much

Best regards
Rose
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 11/26/17 1:08 PM, Roja wrote:

Would you please tell me what is the difference between using umbrella in 4.5.x 
version and 5.1.4 version?are they different in ACCURACY of sampling?


Probably. There have been thousands of bug fixes and features added 
since 4.5.4, which was released 6 years ago. Refer to any and all of the 
release notes in the 4.5.x, 4.6.x, 5.0.x, 5.1.x, and 2016.x series. 
Again, the 4.5.x series is deprecated and officially unsupported.


-Justin


Sent from my iPhone


On Nov 26, 2017, at 21:14, Justin Lemkul  wrote:




On 11/26/17 12:40 PM, rose rahmani wrote:
Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?

Why use deprecated software? We don't officially support the 4.5.x series any 
more. Use the newest version. Some things don't have exact equivalents because 
the pull code was completely re-written a few years ago.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella Sampling

[Roja]

Would you please tell me what is the difference between using umbrella in 4.5.x 
version and 5.1.4 version?are they different in ACCURACY of sampling?

Sent from my iPhone

> On Nov 26, 2017, at 21:14, Justin Lemkul  wrote:
> 
> 
> 
>> On 11/26/17 12:40 PM, rose rahmani wrote:
>> Hello;
>> 
>> what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) 
>> called in version 4.5.4?
> 
> Why use deprecated software? We don't officially support the 4.5.x series any 
> more. Use the newest version. Some things don't have exact equivalents 
> because the pull code was completely re-written a few years ago.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==
> 
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 11/26/17 12:40 PM, rose rahmani wrote:

Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?


Why use deprecated software? We don't officially support the 4.5.x 
series any more. Use the newest version. Some things don't have exact 
equivalents because the pull code was completely re-written a few years ago.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Umbrella Sampling

[rose rahmani]

Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?

Thank you so much
Rose
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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/25/17 3:59 PM, rose rahmani wrote:

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul  wrote:



On 11/25/17 3:07 PM, rose rahmani wrote:


Oh sorry this is .mdp file:

DEFINE   = -DPOSRES


What are you restraining? This seems counterproductive, and by default

(unless you've hacked the topology), this is going to restrain your
protein, which is definitely wrong.

yes, protein.you mean i should remove it and don't restraint anything? and
for npt(previous step) run too?


What is the purpose of a restraint? To prevent motion. What is your 
objective? To cause motion of your protein towards a surface. Does it 
make sense to restrain the protein during this process?


Equilibration is a separate matter.


integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2


Again, I am suspicious of these cutoffs. What force field are you using?

AMBER99


Then yes, those cutoffs are wrong. This is also a very old force field, 
and newer/better variants of it exist. Refer to the literature to find 
the right cutoffs for the parameter set you decide upon. This is not a 
trivial matter.



coulombtype  = pme

cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H


You can probably just use the whole protein here, though I doubt it makes
much difference.

pull_coord1_type= umbrella  ; harmonic biasing force

pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001


Here's your problem. With a positive pull rate, you are instructing mdrun

to increase the COM distance between the protein and the ZnS surface. If
you want them to come closer, you need a negative value here, to decrease
the distance as a function of time. Of course, this all goes out the window
if your protein is restrained, as suggested above.



oh, i've got it.
you restrained chain B in tutorial but i shouldn't because ZnS is freezed?


No, I restrained a chain in my protein to mimic the stability of 
(physiologically) much larger systems. People typically fail to read my 
paper that is the basis of that tutorial, in which this concept is 
explained. Perhaps I need to add a bold, flashing warning that people 
should not be blindly following the method.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Umbrella sampling

[rose rahmani]

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 3:07 PM, rose rahmani wrote:
>
>> Oh sorry this is .mdp file:
>>
>> DEFINE   = -DPOSRES
>>
>
> What are you restraining? This seems counterproductive, and by default
>> (unless you've hacked the topology), this is going to restrain your
>> protein, which is definitely wrong.
>
> yes, protein.you mean i should remove it and don't restraint anything? and
> for npt(previous step) run too?
>
>> integrator   = md
>> dt   = 0.001
>> nsteps   = 200
>> nstxout  = 0
>> nstvout  = 0
>> nstfout  = 0
>> nstlog   = 500
>> nstenergy= 1000
>> nstxtcout= 1000
>> rlist= 1.5
>> rcoulomb = 1.5
>> rvdw = 1.2
>>
>
> Again, I am suspicious of these cutoffs. What force field are you using?
>
> AMBER99
>
> coulombtype  = pme
>> cutoff-scheme= group
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> pcoupl   = no
>> gen-vel  = yes
>> gen-temp = 0
>> gen-seed = 173529
>> constraints  = h-bonds
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrp-excl   = WAL WAL ZnO ZnO
>> energygrps   = SOL WAL ZnO Protein NA CL
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= ZnS
>> pull_group2_name= Protein-H
>>
>
> You can probably just use the whole protein here, though I doubt it makes
> much difference.
>
> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.001
>>
>
> Here's your problem. With a positive pull rate, you are instructing mdrun
>> to increase the COM distance between the protein and the ZnS surface. If
>> you want them to come closer, you need a negative value here, to decrease
>> the distance as a function of time. Of course, this all goes out the window
>> if your protein is restrained, as suggested above.
>
>
oh, i've got it.
you restrained chain B in tutorial but i shouldn't because ZnS is freezed?


> -Justin
>
>
> pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>>
>> On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 11:49 AM, rose rahmani wrote:
>>>
>>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:


 On 11/24/17 3:32 PM, rose rahmani wrote:
>
> I attached md_pull.mdp file
>
>> i put " cutoff-scheme = group" beecause of some errors (about energy
>> groups)
>>
>> The use of energygrps has no effect on the physics. You should view
>>
> pairwise interactions energies as an analysis method, not something
> that
> you need to do as part of your MD run. Don't base your algorithm
> choices
> on
> a quantity that is usually meaningless.
>
> This is what i try to do(part of some literatures);
>
> 1-pulling the CM of the object along the z-axis—perpendicular to the
>> surface of ZnO
>>
>> 2-Pulling is implemented through a “dummy particle” which moves
>> towards
>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>> and drags the CM by the harmonic force corresponding to the spring
>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>> the PMF is averaged laterally
>>
>> 3-The conformations are scanned every 0.1 ps in order to save them
>> with the CM within each of the interval of width 0.05 nm. ( most of
>> all i'm not sure about this part of my mdp file and i don't know how
>> should i implement them).
>>
>> I don't know what .mdp setting you're referring to here.
>>
> Sorry, I didn't understand what you mean?
>
> The mailing list does not accept attachments, so your .mdp file did not
>>> come through. I'm working blind on what settings you're using. What I
>>> specifically don't understand here is your connection between the desired
>>> spacing along the reaction coordinate and whatever .mdp settings you
>>> think
>>> 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/25/17 3:07 PM, rose rahmani wrote:

Oh sorry this is .mdp file:

DEFINE   = -DPOSRES


What are you restraining? This seems counterproductive, and by default 
(unless you've hacked the topology), this is going to restrain your 
protein, which is definitely wrong.



integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2


Again, I am suspicious of these cutoffs. What force field are you using?


coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H


You can probably just use the whole protein here, though I doubt it 
makes much difference.



pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001


Here's your problem. With a positive pull rate, you are instructing 
mdrun to increase the COM distance between the protein and the ZnS 
surface. If you want them to come closer, you need a negative value 
here, to decrease the distance as a function of time. Of course, this 
all goes out the window if your protein is restrained, as suggested above.


-Justin


pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul  wrote:



On 11/25/17 11:49 AM, rose rahmani wrote:


On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:



On 11/24/17 3:32 PM, rose rahmani wrote:

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy
groups)

The use of energygrps has no effect on the physics. You should view

pairwise interactions energies as an analysis method, not something that
you need to do as part of your MD run. Don't base your algorithm choices
on
a quantity that is usually meaningless.

This is what i try to do(part of some literatures);


1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).

I don't know what .mdp setting you're referring to here.

Sorry, I didn't understand what you mean?


The mailing list does not accept attachments, so your .mdp file did not
come through. I'm working blind on what settings you're using. What I
specifically don't understand here is your connection between the desired
spacing along the reaction coordinate and whatever .mdp settings you think
affect this. You can only tell mdrun how frequently to save a frame, you
can't tell it anything about the interval along the reaction coordinate you
care about. Save coordinates frequently enough that you can plausibly
generate a set of configurations to use.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? 

Re: [gmx-users] umbrella sampling

[rose rahmani]

Oh sorry this is .mdp file:

DEFINE   = -DPOSRES
integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnO
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001
pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0




On Sat, Nov 25, 2017 at 11:31 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 12:57 PM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/25/17 5:05 AM, rose rahmani wrote:
>>>
>>> Hi,

 i'm using umbrella sampling and i'm a beginner in GROMACS.

 as an example i got 5 dist.xvg files and then:

 command: perl  distances.pl

> this is distances.pl:
>
 #!/usr/bin/perl -w
 use strict;


 # write output to single file
 open(OUT, ">>summary_distances.dat");

 for (my $j=0; $j<=5; $j++) {
open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91>
 <9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
 #
 @title "Distance"
 @xaxis  label "Time (ps)"
 @yaxis  label "Distance (nm)"
 @TYPE xy
 0.0000.3820.3820.3830.3830.3830.383
 1.178
 0.3820.3820.3830.3830.3830.3830.3830.382
 0.8180.3820.3820.3820.3820.5410.5410.541
 0.5410.5410.5410.5410.5410.5410.5410.541
 0.5410.5410.5410.5410.5410.5410.5410.541
 0.5410.5410.5410.5410.541

Re: [gmx-users] Umbrella sampling

[rose rahmani]

Oh sorry this is .mdp file:

DEFINE   = -DPOSRES
integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnO ZnO
energygrps   = SOL WAL ZnO Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein-H
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.001
pull_coord1_k   = 5000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 11:49 AM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>>
>>> I attached md_pull.mdp file

 i put " cutoff-scheme = group" beecause of some errors (about energy
 groups)

 The use of energygrps has no effect on the physics. You should view
>>> pairwise interactions energies as an analysis method, not something that
>>> you need to do as part of your MD run. Don't base your algorithm choices
>>> on
>>> a quantity that is usually meaningless.
>>>
>>> This is what i try to do(part of some literatures);
>>>
 1-pulling the CM of the object along the z-axis—perpendicular to the
 surface of ZnO

 2-Pulling is implemented through a “dummy particle” which moves towards
 the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
 and drags the CM by the harmonic force corresponding to the spring
 constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
 the PMF is averaged laterally

 3-The conformations are scanned every 0.1 ps in order to save them
 with the CM within each of the interval of width 0.05 nm. ( most of
 all i'm not sure about this part of my mdp file and i don't know how
 should i implement them).

 I don't know what .mdp setting you're referring to here.
>>>
>>> Sorry, I didn't understand what you mean?
>>>
>>
> The mailing list does not accept attachments, so your .mdp file did not
> come through. I'm working blind on what settings you're using. What I
> specifically don't understand here is your connection between the desired
> spacing along the reaction coordinate and whatever .mdp settings you think
> affect this. You can only tell mdrun how frequently to save a frame, you
> can't tell it anything about the interval along the reaction coordinate you
> care about. Save coordinates frequently enough that you can plausibly
> generate a set of configurations to use.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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 

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 11/25/17 12:57 PM, rose rahmani wrote:

On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul  wrote:



On 11/25/17 5:05 AM, rose rahmani wrote:


Hi,

i'm using umbrella sampling and i'm a beginner in GROMACS.

as an example i got 5 dist.xvg files and then:

command: perl  distances.pl

this is distances.pl:

#!/usr/bin/perl -w
use strict;


# write output to single file
open(OUT, ">>summary_distances.dat");

for (my $j=0; $j<=5; $j++) {
   open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91>
<9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
0.0000.3820.3820.3830.3830.3830.383
1.178
0.3820.3820.3830.3830.3830.3830.3830.382
0.8180.3820.3820.3820.3820.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.3820.3820.383
0.3830.3830.3831.1780.3820.3820.3830.383
0.3830.3830.3830.3820.8180.3820.3820.382
0.3820.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.1510.2370.1600.2420.1230.147
~
~

what is my mistake?is that perl script or?! or because of i selected very
close conf.gro files (0-5)?


My Perl script expects each file to have *one* value in it, the COM
distance between two chosen groups. Your output seems to be something else
entirely, suggesting you didn't choose 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/25/17 11:49 AM, rose rahmani wrote:

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:



On 11/24/17 3:32 PM, rose rahmani wrote:


I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy
groups)


The use of energygrps has no effect on the physics. You should view
pairwise interactions energies as an analysis method, not something that
you need to do as part of your MD run. Don't base your algorithm choices on
a quantity that is usually meaningless.

This is what i try to do(part of some literatures);

1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).


I don't know what .mdp setting you're referring to here.

Sorry, I didn't understand what you mean?


The mailing list does not accept attachments, so your .mdp file did not 
come through. I'm working blind on what settings you're using. What I 
specifically don't understand here is your connection between the 
desired spacing along the reaction coordinate and whatever .mdp settings 
you think affect this. You can only tell mdrun how frequently to save a 
frame, you can't tell it anything about the interval along the reaction 
coordinate you care about. Save coordinates frequently enough that you 
can plausibly generate a set of configurations to use.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] umbrella sampling

[rose rahmani]

On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul  wrote:

>
>
> On 11/25/17 5:05 AM, rose rahmani wrote:
>
>> Hi,
>>
>> i'm using umbrella sampling and i'm a beginner in GROMACS.
>>
>> as an example i got 5 dist.xvg files and then:
>>
>> command: perl  distances.pl

>>> this is distances.pl:
>> #!/usr/bin/perl -w
>>use strict;
>>
>>
>># write output to single file
>>open(OUT, ">>summary_distances.dat");
>>
>>for (my $j=0; $j<=5; $j++) {
>>   open(IN, ">   my @array = ;
>>
>>  my $distance;
>>
>>   foreach $_ (@array) {
>>   if ($_ =~ /[#@]/) {
>>   # do nothing, it's a comment
>> or formatting line
>>   } else {
>>   my
>> @line =
>> split(" ", $_);
>>
>>   $distance = $line[1];
>>
>>   }
>>
>>   }
>>
>>
>>   close(IN);
>>
>>   print OUT "$j\t$distance\n";
>>
>>   }
>>
>>
>>   close(OUT);
>>
>>
>>   # clean up
>>
>>   print "Cleaning up...\n";
>>
>>
>>   for (my $k=0; $k<=5; $k++) {
>>
>>   unlink "dist${k}.xvg";
>>
>>   }
>>
>>
>>  exit;
>>
>> but summary-distances.dat:
>>
>> 0   0.382
>> 1   0.382
>> 0   0.382
>> 1   0.382
>> 2   0.382
>> 3   0.382
>> 4   0.382
>> 5   0.382
>> ~
>> ~
>> ~
>>
>> 0.382 is just the first number in dist.xvg files;
>>
>> for example dist0.xvg is:
>>
>> # This file was created Sat Nov 25 04:47:25 2017
>> # Created by:
>> # :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
>> #
>> # Executable:   /usr/local/gromacs/bin/gmx
>> # Data prefix:  /usr/local/gromacs
>> # Command line:
>> #   gmx distance -s pull.tpr -f conf0.gro -n index.ndx -oall dist0.xvg
>> # gmx distance is part of G R O M A C S:
>> #
>> #
>> ¸­°<88><96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91>
>> <9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
>> #
>> @title "Distance"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Distance (nm)"
>> @TYPE xy
>>0.0000.3820.3820.3830.3830.3830.383
>> 1.178
>>0.3820.3820.3830.3830.3830.3830.3830.382
>> 0.8180.3820.3820.3820.3820.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.3820.3820.383
>> 0.3830.3830.3831.1780.3820.3820.3830.383
>> 0.3830.3830.3830.3820.8180.3820.3820.382
>> 0.3820.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.5410.5410.5410.5410.5410.5410.541
>> 0.5410.1510.2370.1600.2420.123

Re: [gmx-users] Umbrella sampling

[rose rahmani]

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul  wrote:

>
>
> On 11/24/17 3:32 PM, rose rahmani wrote:
>
>> I attached md_pull.mdp file
>>
>> i put " cutoff-scheme = group" beecause of some errors (about energy
>> groups)
>>
>
> The use of energygrps has no effect on the physics. You should view
> pairwise interactions energies as an analysis method, not something that
> you need to do as part of your MD run. Don't base your algorithm choices on
> a quantity that is usually meaningless.
>
> This is what i try to do(part of some literatures);
>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>> surface of ZnO
>>
>> 2-Pulling is implemented through a “dummy particle” which moves towards
>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>> and drags the CM by the harmonic force corresponding to the spring
>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>> the PMF is averaged laterally
>>
>> 3-The conformations are scanned every 0.1 ps in order to save them
>> with the CM within each of the interval of width 0.05 nm. ( most of
>> all i'm not sure about this part of my mdp file and i don't know how
>> should i implement them).
>>
>
> I don't know what .mdp setting you're referring to here.
>
> Sorry, I didn't understand what you mean?

>
> 4-between 36-38 conformations should be collected and i dont know how
>> should i choose them between 710 conf.gro files( i got 710
>> conformations after using trajconv)
>>
>
> Calculate the COM distance between the groups for each frame. This is what
> my tutorial does and what my provided scripts help you to analyze. Compile
> a list of the COM distances and determine which frames are suitable for
> starting points of each window.
>
> -Justin
>
>
> this is first part of my job.
>>
>> protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.
>>
>> what do you think about mdp file? where did i make a mistake?
>>
>> Thank you for your attentions (like always ;) )
>>
>> Best Regards
>>
>>
>>
>>
>>
>> Sent from my iPhone
>>
>> On Nov 24, 2017, at 19:34, Justin Lemkul  wrote:
>>>
>>>
>>>
>>> On 11/24/17 9:14 AM, Rose wrote:
 Hello

 I'm beginner in GROMACS. I'm using umbrella sampling(helping from its
 tutorial with MR Lemkul) But I don't know how should I implement deltaZ and
 how choose different conf.gro and which will be useful for further 
 sampling.
 To tell the truth I couldn't get summary.dat by "perl distance.pl"
 command.as I'm not good in programming I couldn't understand what
 happened there?!

>>> Run gmx distance manually. It's probably returning some error, so the
>>> script fails. I've heard this reported a number of times and no one's ever
>>> told me what the solution is, so unfortunately there's nothing I can do to
>>> fix it.
>>>
>>> How did you know for example:
 50>>>0.6 nm
 100>>>0.8 nm

>>> This is what gmx distance computes.
>>>
>>> I need deltaz=0.05nm

>>> Then you will need to save frames very frequently. This is a very narrow
>>> dz, and may be overkill depending on what the system is.
>>>
>>> Please help me, i don't know where should i find these informations and
 modify them.

 2- I want that reaction coordinate across Z axes, from slab to 1.5nm
 far from it (and rvdw and coulomb=1.5 and

>>> What force field uses such a cutoff? Don't make ad hoc changes to the
>>> cutoffs used by any given force field, as you will get unexpected (or
>>> invalid) results...
>>>
>>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer
 to wall(4nm far from slab) except slab.
 What is my mistake?!

>>> You'll have to provide an .mdp file and a complete description of your
>>> system, how you constructed it, and what your objectives are. Images would
>>> help.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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.
>>>
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> 

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 11/25/17 5:05 AM, rose rahmani wrote:

Hi,

i'm using umbrella sampling and i'm a beginner in GROMACS.

as an example i got 5 dist.xvg files and then:


command: perl  distances.pl

this is distances.pl:
#!/usr/bin/perl -w
   use strict;


   # write output to single file
   open(OUT, ">>summary_distances.dat");

   for (my $j=0; $j<=5; $j++) {
  open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91><9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
   0.0000.3820.3820.3830.3830.3830.3831.178
   0.3820.3820.3830.3830.3830.3830.3830.382
0.8180.3820.3820.3820.3820.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.3820.3820.383
0.3830.3830.3831.1780.3820.3820.3830.383
0.3830.3830.3830.3820.8180.3820.3820.382
0.3820.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.1510.2370.1600.2420.1230.147
~
~

what is my mistake?is that perl script or?! or because of i selected very
close conf.gro files (0-5)?


My Perl script expects each file to have *one* value in it, the COM 
distance between two chosen groups. Your output seems to be something 
else entirely, suggesting you didn't choose appropriate groups.



i selected them just for testing my script and to tell the truth i didn't
know how use gmx distance to get all 718 

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/24/17 3:32 PM, rose rahmani wrote:

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy groups)


The use of energygrps has no effect on the physics. You should view 
pairwise interactions energies as an analysis method, not something that 
you need to do as part of your MD run. Don't base your algorithm choices 
on a quantity that is usually meaningless.



This is what i try to do(part of some literatures);
1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).


I don't know what .mdp setting you're referring to here.


4-between 36-38 conformations should be collected and i dont know how
should i choose them between 710 conf.gro files( i got 710
conformations after using trajconv)


Calculate the COM distance between the groups for each frame. This is 
what my tutorial does and what my provided scripts help you to analyze. 
Compile a list of the COM distances and determine which frames are 
suitable for starting points of each window.


-Justin


this is first part of my job.

protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.

what do you think about mdp file? where did i make a mistake?

Thank you for your attentions (like always ;) )

Best Regards





Sent from my iPhone


On Nov 24, 2017, at 19:34, Justin Lemkul  wrote:




On 11/24/17 9:14 AM, Rose wrote:
Hello

I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial 
with MR Lemkul) But I don't know how should I implement deltaZ and how choose 
different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as 
I'm not good in programming I couldn't understand what happened there?!

Run gmx distance manually. It's probably returning some error, so the script 
fails. I've heard this reported a number of times and no one's ever told me 
what the solution is, so unfortunately there's nothing I can do to fix it.


How did you know for example:
50>>>0.6 nm
100>>>0.8 nm

This is what gmx distance computes.


I need deltaz=0.05nm

Then you will need to save frames very frequently. This is a very narrow dz, 
and may be overkill depending on what the system is.


Please help me, i don't know where should i find these informations and modify 
them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from 
it (and rvdw and coulomb=1.5 and

What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs 
used by any given force field, as you will get unexpected (or invalid) 
results...


rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to 
wall(4nm far from slab) except slab.
What is my mistake?!

You'll have to provide an .mdp file and a complete description of your system, 
how you constructed it, and what your objectives are. Images would help.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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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mail to gmx-users-requ...@gromacs.org.




--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] umbrella sampling

[rose rahmani]

Hi,

i'm using umbrella sampling and i'm a beginner in GROMACS.

as an example i got 5 dist.xvg files and then:

>>command: perl  distances.pl

this is distances.pl:
#!/usr/bin/perl -w
  use strict;


  # write output to single file
  open(OUT, ">>summary_distances.dat");

  for (my $j=0; $j<=5; $j++) {
 open(IN, "<96><91><98>ò<90><91><8c><8b><9a><8d><8c>þ<91><9b>ü<93><90><91><96><91><98>ì<97><8d><96><92><8f><8c>
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
  0.0000.3820.3820.3830.3830.3830.3831.178
  0.3820.3820.3830.3830.3830.3830.3830.382
0.8180.3820.3820.3820.3820.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.3820.3820.383
0.3830.3830.3831.1780.3820.3820.3830.383
0.3830.3830.3830.3820.8180.3820.3820.382
0.3820.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.5410.5410.5410.5410.5410.5410.541
0.5410.1510.2370.1600.2420.1230.147
~
~

what is my mistake?is that perl script or?! or because of i selected very
close conf.gro files (0-5)?
i selected them just for testing my script and to tell the truth i didn't
know how use gmx distance to get all 718 (configuration's) xvg files with
just ONE command so i have to get .xvg files one by one.(would you please
tell me?)


- it's much similar to tutorial's(by Mr Lemkul) perl script but not as same
as it because i got some errors so i had to use gmx distance separately.

Best Regards

Rose
-- 

Re: [gmx-users] Umbrella sampling

[rose rahmani]

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy groups)

This is what i try to do(part of some literatures);
1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).

4-between 36-38 conformations should be collected and i dont know how
should i choose them between 710 conf.gro files( i got 710
conformations after using trajconv)

this is first part of my job.

protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.

what do you think about mdp file? where did i make a mistake?

Thank you for your attentions (like always ;) )

Best Regards





Sent from my iPhone

> On Nov 24, 2017, at 19:34, Justin Lemkul  wrote:
>
>
>
>> On 11/24/17 9:14 AM, Rose wrote:
>> Hello
>>
>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its 
>> tutorial with MR Lemkul) But I don't know how should I implement deltaZ and 
>> how choose different conf.gro and which will be useful for further sampling.
>> To tell the truth I couldn't get summary.dat by "perl distance.pl" 
>> command.as I'm not good in programming I couldn't understand what happened 
>> there?!
>
> Run gmx distance manually. It's probably returning some error, so the script 
> fails. I've heard this reported a number of times and no one's ever told me 
> what the solution is, so unfortunately there's nothing I can do to fix it.
>
>> How did you know for example:
>> 50>>>0.6 nm
>> 100>>>0.8 nm
>
> This is what gmx distance computes.
>
>> I need deltaz=0.05nm
>
> Then you will need to save frames very frequently. This is a very narrow dz, 
> and may be overkill depending on what the system is.
>
>> Please help me, i don't know where should i find these informations and 
>> modify them.
>>
>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far 
>> from it (and rvdw and coulomb=1.5 and
>
> What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs 
> used by any given force field, as you will get unexpected (or invalid) 
> results...
>
>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to 
>> wall(4nm far from slab) except slab.
>> What is my mistake?!
>
> You'll have to provide an .mdp file and a complete description of your 
> system, how you constructed it, and what your objectives are. Images would 
> help.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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.
-- 
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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/24/17 9:14 AM, Rose wrote:

Hello

I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial 
with MR Lemkul) But I don't know how should I implement deltaZ and how choose 
different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as 
I'm not good in programming I couldn't understand what happened there?!


Run gmx distance manually. It's probably returning some error, so the 
script fails. I've heard this reported a number of times and no one's 
ever told me what the solution is, so unfortunately there's nothing I 
can do to fix it.



How did you know for example:
50>>>0.6 nm
100>>>0.8 nm


This is what gmx distance computes.


I need deltaz=0.05nm


Then you will need to save frames very frequently. This is a very narrow 
dz, and may be overkill depending on what the system is.



Please help me, i don't know where should i find these informations and modify 
them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from 
it (and rvdw and coulomb=1.5 and


What force field uses such a cutoff? Don't make ad hoc changes to the 
cutoffs used by any given force field, as you will get unexpected (or 
invalid) results...



rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to 
wall(4nm far from slab) except slab.
What is my mistake?!


You'll have to provide an .mdp file and a complete description of your 
system, how you constructed it, and what your objectives are. Images 
would help.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

[gmx-users] Umbrella sampling

[Rose]

Hello

I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial 
with MR Lemkul) But I don't know how should I implement deltaZ and how choose 
different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as 
I'm not good in programming I couldn't understand what happened there?!
How did you know for example:
50>>>0.6 nm
100>>>0.8 nm

I need deltaz=0.05nm 

Please help me, i don't know where should i find these informations and modify 
them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from 
it (and rvdw and coulomb=1.5 and rlist=1.2) but it moves from1.5nm to for 
example 3nm and getting closer to wall(4nm far from slab) except slab.
What is my mistake?!

I really need your help.

Best Regards

Rose

Sent from my iPhone
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[gmx-users] Umbrella Sampling

[rose rahmani]

Hello;

i'm using umbrella sampling and i have some basic questions about it, i
will appreciate you if you help me;

1. for example i've got 2000 conf.gro and i want to choose  38 of them.  i
dont know how choose them eficiently???(The conformations are scanned every
0.1 ps in order to save them with the CM within each of the interval of
width 0.05 nm)

2. where should i implement this " 0.1 ps " >>>what is called in mdp file?
3. how should i know that width is 0.05 between different configurations?

best regards
Rose
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[gmx-users] Umbrella Sampling

[rose rahmani]

Hello;

i'm using umbrella sampling and i have some basic questions about it, i
will appreciate you if you help me;

1. for example i've got 2000 conf.gro and i want to choose  38 of them.  i
dont know how choose them eficiently???(The conformations are scanned every
0.1 ps in order to save them with the CM within each of the interval of
width 0.05 nm)

2. where should i implement this " 0.1 ps " >>>what is called in mdp file?
3. how should i know that width is 0.05 between different configurations?

best regards
ROSE
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[gmx-users] Umbrella Sampling

[rose rahmani]

Hello

i'm trying to do umbrella sampling and
 this is md_umbrella.mdp;
DEFINE   = -DPOSRES
integrator   = md
dt   = 0.001
nsteps   = 4000
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 5000
nstenergy= 1
nstxtcout= 1
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
-
when i use grompp i get this erro and notes;

NOTE 1 [file md_umbrella.mdp, line 52]:
  md_umbrella.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.

Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#

ERROR 1 [file md_umbrella.mdp]:
  With Verlet lists rcoulomb!=rvdw is not supported


NOTE 2 [file md_umbrella.mdp]:
  Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off
  and vdw_modifier=Potential-switch

i used version 4.5.4  before grompp and i think this error comes from
using  gmx,but i dont know how EXACTLY should i change mdp file when i us
gmx. (i want to move protein toward ZnS and protein is 1.5nm far from ZnS
at t=0 and both of them are in center of simulation box at t=0).

thank you so much

best regards
rose
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[gmx-users] Umbrella Sampling

[rose rahmani]

Hello

i'm trying to do umbrella sampling and
 this is  part of md_umbrella.mdp;
DEFINE   = -DPOSRES
integrator   = md
dt   = 0.001
nsteps   = 4000
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 5000
nstenergy= 1
nstxtcout= 1
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
-
when i use grompp i get this erro and notes;

NOTE 1 [file md_umbrella.mdp, line 52]:
  md_umbrella.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.

Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#

ERROR 1 [file md_umbrella.mdp]:
  With Verlet lists rcoulomb!=rvdw is not supported


NOTE 2 [file md_umbrella.mdp]:
  Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off
  and vdw_modifier=Potential-switch

i used version 4.5.4  before grompp and i think this error comes from
using  gmx,but i dont know how EXACTLY should i change mdp file when i us
gmx. (i want to move protein toward ZnS and protein is 1.5nm far from ZnS
at t=0 and both of them are in center of simulation box at t=0).

thank you so much

best regards
rose
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[gmx-users] Umbrella Sampling Replica Exchange

[Hermann, Johannes]

Dear all,

I was surprised that my Google search for Replica Exchange for Umbrella 
sampling using Gromacs did not yield a positive result.


Is it really not possible to perform HRE for US within the framework of 
Gromacs?


Thanks in advance for any answer, hint, or tutorial!

All the best

Johannes

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Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
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Re: [gmx-users] Umbrella sampling: issue with COM distance far from initial value

[Wes Barnett]

On Tue, Oct 17, 2017 at 8:05 AM, Giuseppe Léonardo Licari <
giuseppe.lic...@unige.ch> wrote:

> Dear all,
>
> I have troubles with umbrella sampling. During the umbrella sampling
> simulation the COM distance between the two solutes is going too far from
> the set initial value. I tried to increase a lot the force constant of the
> harmonic potential. I also tried to change "umbrella" to "contraint", with
> no success. How can I fix the COM distance between the two solutes? It
> seems that increasing the force constant does not work. Am I making some
> mistake in the input? I have Gromacs v. 5.1.2 and here you can find the
> files of a test simulation:
>
> https://www.dropbox.com/s/cl7au3twx8d6iip/test.zip?dl=0
>
> As you see from the trajectory the two solutes go very far from the
> initial COM distance. Does somebody have an idea about this?
>
> Thanks for the help and have a nice day.
> Regards,
> Licari
> Giuseppe
>

I viewed the trajectory, but I can't see anything wrong. The two solutes
seem to maintain a COM to COM distance that they started with. Note you are
only doing the pull code on the z-vector so they are allowed to move as far
as they want in the x and y directions from each other. Also your are using
direction-periodic, which is probably not what you want.

Use a bigger box, and use the distance method, or if you want to just do it
along the z-vector (with direction, not direction-periodic) you will
probably have to use a flat-bottom restraint to keep your solutes along the
z-axis.

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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[gmx-users] Umbrella sampling: issue with COM distance far from initial value

[Giuseppe Léonardo Licari]

Dear all,

I have troubles with umbrella sampling. During the umbrella sampling simulation 
the COM distance between the two solutes is going too far from the set initial 
value. I tried to increase a lot the force constant of the harmonic potential. 
I also tried to change "umbrella" to "contraint", with no success. How can I 
fix the COM distance between the two solutes? It seems that increasing the 
force constant does not work. Am I making some mistake in the input? I have 
Gromacs v. 5.1.2 and here you can find the files of a test simulation:

https://www.dropbox.com/s/cl7au3twx8d6iip/test.zip?dl=0

As you see from the trajectory the two solutes go very far from the initial COM 
distance. Does somebody have an idea about this?

Thanks for the help and have a nice day.
Regards,
Licari
Giuseppe

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[gmx-users] umbrella sampling

[Shaoqi Zhan]

??Hi gmx-users,


I am running umbrella sampling according to the gromacs tutorial written by 
Justin A. Lemkul. In my system, there are two molecules (Chain_A and Chain_B) 
immobilized on the CNT surface with pi-stacking. I would like to calculate PMF 
of these two molecules (on the CNT surface) by using umbrella sampling, which 
means the CNT will be restrained and run umbrella sampling for two molecules 
(restrain one of molecules, then pull another molecule to move on the CNT 
surface). I use the .mdp file as follow:


title   = Umbrella pulling simulation
define  = -DPOSRES  ; position restraint the cnt
; Run parameters
integrator  = md
dt  = 0.001
tinit   = 0
nsteps  = 10;
nstcomm = 10
; Output parameters
nstxout = 5000  ;
nstvout = 5000
nstfout = 500
nstxtcout   = 500   ;
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = System
tau_t   = 0.5
ref_t   = 300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= yes
pull_ngroups= 3
pull_ncoords= 1
pull_group1_name= CNT
pull_group2_name= Chain_A
pull_group3_name= Chain_B
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  =  2 3
pull_coord1_dim = Y Y Y
pull_coord1_rate= 0.005  ; 0.005 nm per ps = 1 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0

no matter which ''pull_coord1_dim'' I use (Y N N or the others), decrease 
timestep from 2fs to 1fs or decrease the force tolerance values from 1000 to 
100 in .mdp file of minimization. I always meet an fatal error "step 216: Water 
molecule starting at atom 2453 can not be settled. Check for bad contacts 
and/or reduce the timestep if appropriate."
And when I run regular MD simulation with gromacs for this system, it doesn't 
meet any error. But when I run umbrella sampling, it alsways meet an error at 
step of generate configurations. Could you please help me solve this problem?  
Thanks.

Best,
Shaoqi Zhan







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[gmx-users] umbrella sampling

[Nivedita Rai]

Dear gromacs developers,

I am trying to implement umbrella sampling in my work but instead of
distance pulling i want to do rotational pull with the gap of 10 degree. I
went through your tutorial and many articles but im unable to find  how to
implement rotational pull in .mdp file. will you please guide me or send me
any article which i can refer for my objective.


-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 9/2/17 10:28 AM, sp...@iacs.res.in wrote:

  Hi all
I am trying to do umbrella sampling of protein unfolding with radius of
gyration as reaction coordinate using gromacs-2016.3 patched with
plumed-2.3.2. I want to calculate free energy for the system. I am using
the following command

gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat  free.dat



None of this is valid syntax.


It shows an error
  Fatal error:
  Give either pullx (-ix) OR pullf (-if) data. Not both.

But I am using radius of gyration as variable.Why I need to give pullx ?
Please anyone help.



gmx wham assumes you're using the GROMACS pull code, therefore relying entirely 
on GROMACS input and output files.  If you're doing something else, you're going 
to need to use another program (e.g. Alan Grossfield's WHAM program or whatever 
else the PLUMED community suggests).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] umbrella sampling

[spss4]

 Hi all
I am trying to do umbrella sampling of protein unfolding with radius of
gyration as reaction coordinate using gromacs-2016.3 patched with
plumed-2.3.2. I want to calculate free energy for the system. I am using
the following command

gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat  free.dat

It shows an error 
 Fatal error:
 Give either pullx (-ix) OR pullf (-if) data. Not both.

But I am using radius of gyration as variable.Why I need to give pullx ?
Please anyone help.
  
Thanks
  
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[gmx-users] umbrella sampling

[spss4]

Hi all
I am trying to do umbrella sampling of protein with radius of gyration as
reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I have
chosen 13 configurations of protein for sampling. Now I want to analyse the
data. So how to plot histogram and PMF w.r.t radius of gyartion? Can anyone
help me? I am new in this field.

Thanks
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[gmx-users] Umbrella Sampling -PME

[mohamed mehana]

Hello,
will decouple intramuscular interactions during windows simulation impact
the accuracy of the PME estimated?
I am pulling large molecule
Regards
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[gmx-users] Umbrella Sampling with Direction-Periodic

[Daniel Kozuch]

Hello,

I am using a pull code with geometry=direction-periodic and attempting to
use gmx wham to construct the free energy. The pulling code is doing what I
would like it to, but as might be expected from direction-periodic, when
the pull distance is more than half the box length the distance is written
as negative.

Is there some way to have the pull files written with positive (greater
than half the box length) distance so that gmx wham will work properly? For
example, if the box is 10 nm long, I would like the pull distance to be
written as 7 nm, not -3 nm.

I have tried editing the pullx.xvg files, but as the .tpr files must still
include the original shortest periodic distance, this does not correct the
issue.

Thanks,
Dan
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[gmx-users] Umbrella Sampling with Direction-Periodic Pulling

[Daniel Kozuch]

Hello,

I am using a pull code with geometry=direction-periodic and attempting to
use gmx wham to construct the free energy. I believe the pulling code is
doing what I would like it to, but as might be expected from
direction-periodic, when the pull distance is more than half the box length
the distance is written as negative.

Is there some way to have the pull files written with positive (greater
than half the box length) distance so that gmx wham will work properly? For
example, if the box is 10 nm long, I would like the pull distance to be
written as 7 nm, not -3 nm. Or is the best option to simply edit the pullx
files?

Thanks,
Dan
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 5:29 PM, Ben Tam wrote:

Hi Justin,

Thanks for answering. I have tried sending the histogram however it is too big 
of a file. But the histogram shows a lot of overlapping and multiple peaks. All 
of the value in profile.xvg  showing nan. What can that mean?




Most likely a sampling problem.  But as I cannot see your histograms, I can't 
guess any further at specifically what's going on.


-Justin

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==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 1:38 PM, Ben Tam wrote:

Hi Justin,


I am trying to get an energy profile when water molecules go through the porous 
cage. I am restraint it to z direction because I would like to see the energy 
that require to jump from one cage to another. I set up the simulation so that 
the structure is repeated at z direction which this will give me more sample 
slice for starting configuration. Sorry I am still new to the umbrella sampling.



OK, I see what you're doing now.  That should be fine, but without seeing the 
histograms it's impossible to know how well things are working.  If you're 
getting NaN somewhere, that means a gap in the sampling.


-Justin



Best regards,


Ben





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling



On 7/11/17 12:53 PM, Ben Tam wrote:

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework 
that I am working on which is a porous material. With the k value larger than 
100, the histogram become multiple sharp single peak.

Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".




I'm really confused about your setup.  From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z.  What is
the geometry of your system?  Don't follow my tutorial too closely, it's not
appropriate for most cases...

-Justin



Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias de 
Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:


Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?

Best regards,

Ben


--
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* Please search the archive at http://www.gromacs.org/Support



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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==

Re: [gmx-users] umbrella sampling

[Ben Tam]

Hi Justin,


I am trying to get an energy profile when water molecules go through the porous 
cage. I am restraint it to z direction because I would like to see the energy 
that require to jump from one cage to another. I set up the simulation so that 
the structure is repeated at z direction which this will give me more sample 
slice for starting configuration. Sorry I am still new to the umbrella sampling.


Best regards,


Ben





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling



On 7/11/17 12:53 PM, Ben Tam wrote:
> Hi Andre,
>
>
> Thanks for your answer. Actually I should clarify it is 
> metal-organic-framework that I am working on which is a porous material. With 
> the k value larger than 100, the histogram become multiple sharp single peak.
Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".
>

I'm really confused about your setup.  From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z.  What is
the geometry of your system?  Don't follow my tutorial too closely, it's not
appropriate for most cases...

-Justin

>
> Best regards,
>
>
> Ben
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias 
> de Moura <mo...@ufscar.br>
> Sent: Tuesday, July 11, 2017 17:44
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] umbrella sampling
>
> I never did it myself, but generally speaking you don' t expect that there'
> s a lot of room inside a crystal for any molecule to diffuse there,
> especially when it comes to cross something like a crystallographic plane,
> meaning that huge energy barriers should be there, leading to NaN and other
> weird numerical issues.
>
> in principle, larger force constants might help you to sample high energy
> barrier, but it will be most likely a trial and error procedure until you
> fine-tune the forces along the profile.
>
> best
>
> Andre
>
> On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:
>
>> Dear All,
>>
>> I am doing umbrella sampling for a water molecules moving inside a crystal
>> structure, however I am running into a problem on the output file with
>> profile.xvg all value showing “nan”. This error has occurred when I reduce
>> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
>> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
>> code I used is the following:
>>
>> ;Pull code
>> pull = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = MOL
>> pull_group2_name = SOL
>> pull_coord1_type = umbrella ; harmonic biasing force
>> pull_coord1_geometry = distance ; simple distance increase
>> ;pull_coord1_vec = 0 0 1
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes ; define initial COM distance > 0
>>
>> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
>> have tried increasing the k value to 50 and 100 with the same results.
>>
>> The histogram shows many overlap, however when I use k value 100, it is
>> only giving me individual single peak. Therefore can someone enlighten on
>> what is going on?
>>
>> Best regards,
>>
>> Ben
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support

> Support - Gromacs<http://www.gromacs.org/Support>

> www.gromacs.org<http://www.gromacs.org>
> When posting a request for assistance to the Mailing Lists, be sure to. cite 
> your GROMACS version number (and if it's not the most recent, try installing 
> that first!),
>
>
>
>> /Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 12:53 PM, Ben Tam wrote:

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework that I am working on which is a porous material. With the k value larger than 100, the histogram become multiple sharp single peak. 
Furthermore when I look at individual 0.1nm slides, it runs completely fine 
without obvious anomaly. Therefore I am really confused why the profile.xvg 
become infinite or "nan".




I'm really confused about your setup.  From what it sounds like, your windows 
are too narrow to get good sampling, perhaps the force constant is too strong, 
and I'm really not sure why you're only applying a restraint along z.  What is 
the geometry of your system?  Don't follow my tutorial too closely, it's not 
appropriate for most cases...


-Justin



Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias de 
Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:


Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?

Best regards,

Ben


--
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* Please search the archive at http://www.gromacs.org/Support

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--
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
--
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* Please search the archive at 
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Re: [gmx-users] umbrella sampling

[Ben Tam]

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework 
that I am working on which is a porous material. With the k value larger than 
100, the histogram become multiple sharp single peak. Furthermore when I look 
at individual 0.1nm slides, it runs completely fine without obvious anomaly. 
Therefore I am really confused why the profile.xvg become infinite or "nan".


Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias 
de Moura <mo...@ufscar.br>
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote:

> Dear All,
>
> I am doing umbrella sampling for a water molecules moving inside a crystal
> structure, however I am running into a problem on the output file with
> profile.xvg all value showing “nan”. This error has occurred when I reduce
> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
> code I used is the following:
>
> ;Pull code
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = MOL
> pull_group2_name = SOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> ;pull_coord1_vec = 0 0 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
> have tried increasing the k value to 50 and 100 with the same results.
>
> The histogram shows many overlap, however when I use k value 100, it is
> only giving me individual single peak. Therefore can someone enlighten on
> what is going on?
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
Support - Gromacs<http://www.gromacs.org/Support>
www.gromacs.org
When posting a request for assistance to the Mailing Lists, be sure to. cite 
your GROMACS version number (and if it's not the most recent, try installing 
that first!),



> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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The three mailing lists (see the menu items on the left) have slightly 
different purposes, and you might not be interested in subscribing to all of 
them:



>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>



--
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
--
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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Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
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...<https://maillist.sys.kth.se/m

Re: [gmx-users] umbrella sampling

[André Farias de Moura]

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:

> Dear All,
>
> I am doing umbrella sampling for a water molecules moving inside a crystal
> structure, however I am running into a problem on the output file with
> profile.xvg all value showing “nan”. This error has occurred when I reduce
> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
> code I used is the following:
>
> ;Pull code
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = MOL
> pull_group2_name = SOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> ;pull_coord1_vec = 0 0 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
> have tried increasing the k value to 50 and 100 with the same results.
>
> The histogram shows many overlap, however when I use k value 100, it is
> only giving me individual single peak. Therefore can someone enlighten on
> what is going on?
>
> Best regards,
>
> Ben
>
>
> --
> 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.
>



-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
-- 
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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] umbrella sampling

[Ben Tam]

Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal 
structure, however I am running into a problem on the output file with 
profile.xvg all value showing “nan”. This error has occurred when I reduce the 
slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for 0.2 and 
0.1, however only 0.2 has given me meaningful profile. The pull code I used is 
the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I have 
tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is only 
giving me individual single peak. Therefore can someone enlighten on what is 
going on?

Best regards,

Ben


-- 
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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 6/14/17 10:52 PM, Kingsley Theras Primus Dass . wrote:

Hii
  I am trying out the umbrella sampling tutorial. I finished generating a
series of coordinate file , but when i run the perl script the
summary_distance.dat doesnt generate the COM distance value 
What would be the possible reason for this ?



People keep reporting this and I never find out why, but the advice is the same 
- abandon the script and try one of the calls to gmx distance yourself.  It will 
print an error that you can diagnose.  Probably your index file isn't set up 
correctly.  If you do work it out, please report back so I know if there's 
actually something wrong (the script itself is quite trivial so I know that's 
not the problem, but maybe something about the call to gmx distance is).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling

[Kingsley Theras Primus Dass .]

Hii
 I am trying out the umbrella sampling tutorial. I finished generating a
series of coordinate file , but when i run the perl script the
summary_distance.dat doesnt generate the COM distance value 
What would be the possible reason for this ?

Thank you
Kingsley
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Alex]

>
>
>>
> A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.


The pull vector is exactly as set by you to N N Y, maybe the code
multiplies the vector components by the corresponding pull rates and then
checks the resulting velocity vector, I don't know, but the error is there
with 5.1.*,. No error when using GMX 5.0.4 i have on a local machine, btw.
I'll get back to you on the exact input file and the GMX version.


>
>>>

 Old GROMACS versions had a "position" geometry that was the go-to for
>>> membrane/slab/layered systems and worked quite nicely, but that's gone
>>> now,
>>> replaced by other options that I've never used.
>>>
>>
>>
>> How old? I have 5.0.4 on another machine here...
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/2/17 6:40 PM, Alex wrote:


I find that surprising.  Please provide the full, exact error and your

pull settings.  All of the geometries should work with zero or non-zero
pull rates. But I admit, it has been many years since I used GROMACS with
the pull code.




Simply take your pull code from the tutorial and replace 'distance' with
'direction-periodic' or 'cylinder' (along with some r0/r1). The error is
that the pull vector cannot be (0 0 0), do not remember the exact text.


A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.


Setting the pull rate to something like 1e-12 results in the same error.
Our cluster is down for maintenance until Monday, will give you the exact
excerpt, if needed.



If you want to troubleshoot further, yes.

-Justin








Old GROMACS versions had a "position" geometry that was the go-to for
membrane/slab/layered systems and worked quite nicely, but that's gone now,
replaced by other options that I've never used.



How old? I have 5.0.4 on another machine here...



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Alex]

>
> I find that surprising.  Please provide the full, exact error and your
>> pull settings.  All of the geometries should work with zero or non-zero
>> pull rates. But I admit, it has been many years since I used GROMACS with
>> the pull code.
>>
>
Simply take your pull code from the tutorial and replace 'distance' with
'direction-periodic' or 'cylinder' (along with some r0/r1). The error is
that the pull vector cannot be (0 0 0), do not remember the exact text.
Setting the pull rate to something like 1e-12 results in the same error.
Our cluster is down for maintenance until Monday, will give you the exact
excerpt, if needed.

>
>
>>
>>
> Old GROMACS versions had a "position" geometry that was the go-to for
> membrane/slab/layered systems and worked quite nicely, but that's gone now,
> replaced by other options that I've never used.


How old? I have 5.0.4 on another machine here...
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/2/17 4:17 PM, Alex wrote:

So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my


I find that surprising.  Please provide the full, exact error and your pull 
settings.  All of the geometries should work with zero or non-zero pull rates. 
But I admit, it has been many years since I used GROMACS with the pull code.



particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup? I'd understand if the entire membrane was reactive, but it
isn't. Also, the obtained free energy value is very close to what one gets
by simply integrating the pullf data wrt pull coordinate, which makes
perfect sense. Any comments/suggestions?



You might get some windows that conveniently work with "simpler" settings but I 
still think you need to do what I said before.  Old GROMACS versions had a 
"position" geometry that was the go-to for membrane/slab/layered systems and 
worked quite nicely, but that's gone now, replaced by other options that I've 
never used.


-Justin


Thanks,

Alex

On Fri, Jun 2, 2017 at 11:26 AM, Alex  wrote:







Yes, because if your ion diffuses laterally (or whatever constitutes your
"hole"), then you're not sampling what you think you're sampling.  That's
what the cylinder geometry is for.  You have a system capable of
significant lateral movement, so if you fail to apply a bias that acts in
the x-y plane, your results are very quickly going to become garbage.

-Justin

Of course. I actually realized that you used COM distance and not e.g.

direction-periodic (which won't accept zero pulling rates anyway) only
after I asked.
Specifying somewhat awkward structures like disks as references could be
avoided by simply allowing a component of the COM distance vector and not
the entire vector) to be used. Anyway, doesn't really matter.

Thanks,

Alex



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] Umbrella sampling and PMF calculations

[Alex]

So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup? I'd understand if the entire membrane was reactive, but it
isn't. Also, the obtained free energy value is very close to what one gets
by simply integrating the pullf data wrt pull coordinate, which makes
perfect sense. Any comments/suggestions?

Thanks,

Alex

On Fri, Jun 2, 2017 at 11:26 AM, Alex  wrote:

>
>
>>>
>> Yes, because if your ion diffuses laterally (or whatever constitutes your
>> "hole"), then you're not sampling what you think you're sampling.  That's
>> what the cylinder geometry is for.  You have a system capable of
>> significant lateral movement, so if you fail to apply a bias that acts in
>> the x-y plane, your results are very quickly going to become garbage.
>>
>> -Justin
>>
>> Of course. I actually realized that you used COM distance and not e.g.
> direction-periodic (which won't accept zero pulling rates anyway) only
> after I asked.
> Specifying somewhat awkward structures like disks as references could be
> avoided by simply allowing a component of the COM distance vector and not
> the entire vector) to be used. Anyway, doesn't really matter.
>
> Thanks,
>
> Alex
>
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Alex]

Yes, because if your ion diffuses laterally (or whatever constitutes 
your "hole"), then you're not sampling what you think you're 
sampling.  That's what the cylinder geometry is for.  You have a 
system capable of significant lateral movement, so if you fail to 
apply a bias that acts in the x-y plane, your results are very quickly 
going to become garbage.


-Justin

Of course. I actually realized that you used COM distance and not e.g. 
direction-periodic (which won't accept zero pulling rates anyway) only 
after I asked.
Specifying somewhat awkward structures like disks as references could be 
avoided by simply allowing a component of the COM distance vector and 
not the entire vector) to be used. Anyway, doesn't really matter.


Thanks,

Alex
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/1/17 6:35 PM, Alex wrote:






You have a membrane with water on either side, yes?  That's a layered
system.

But frankly, at this point I don't follow at all what you're trying to do.

-


Let me try from the beginning. :)
A membrane in XY, water on both sides. At the center of the membrane, there
is a geometrically symmetric hole. A series of configurations exists,
starting with the ion at +Z_0 above the membrane (along Z) and ending at
-Z_0 below, only the Z coordinate is varying here. The center of the hole
and the XY-position of the ion are very close, i.e. things are aligned (the
series of configurations was generated in a pull simulation with the ion
restrained in XY and pulled along Z). The goal is to find the free energy
associated with ion's binding to the interior of the hole in membrane,
nothing else. I can share the trajectory (without -sep), but only
privately. Does this make sense?

Is there any reason you think I _cannot_ use your approach pretty much
directly?



Yes, because if your ion diffuses laterally (or whatever constitutes your 
"hole"), then you're not sampling what you think you're sampling.  That's what 
the cylinder geometry is for.  You have a system capable of significant lateral 
movement, so if you fail to apply a bias that acts in the x-y plane, your 
results are very quickly going to become garbage.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] Umbrella sampling and PMF calculations

[Alex]

>
>
>>
> You have a membrane with water on either side, yes?  That's a layered
> system.
>
> But frankly, at this point I don't follow at all what you're trying to do.
>
> -

Let me try from the beginning. :)
A membrane in XY, water on both sides. At the center of the membrane, there
is a geometrically symmetric hole. A series of configurations exists,
starting with the ion at +Z_0 above the membrane (along Z) and ending at
-Z_0 below, only the Z coordinate is varying here. The center of the hole
and the XY-position of the ion are very close, i.e. things are aligned (the
series of configurations was generated in a pull simulation with the ion
restrained in XY and pulled along Z). The goal is to find the free energy
associated with ion's binding to the interior of the hole in membrane,
nothing else. I can share the trajectory (without -sep), but only
privately. Does this make sense?

Is there any reason you think I _cannot_ use your approach pretty much
directly?

Thanks,

Alex
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/1/17 6:16 PM, Alex wrote:






Your situation is completely different.  Look into the cylinder settings
for dealing with a layered system, but I have no experience with them.  To
be clear - you always need two groups to define the vector (reaction
coordinate) along which the bias is applied.  So you need to define a
second group; you can't just say "I'm biasing an ion and that's it."



Okay, I see. However, I have a pretty simple situation: an ion and the rest
of the system, i.e. a membrane with all the atoms it contains, water, and a
counterion to the ion of interest -- which could be the groups in question,
after I use make_ndx properly. The simulations that result in the
pullf/pullx data of interest are using "pseudo" pull, because your pulling
rate is set to zero, so in terms of moving things, nothing actually gets
pulled and this is merely a way of obtaining the pullf data in the
direction of the bias. It sounds like there is little difference between
our systems. My topology of the ion of interest has no restraint in the
Z-direction, i.e. indeed a cylinder type of constraint in-plane. So, when
you say that my situation is completely different, what do you mean? There
is really nothing "layered" about my system...



You have a membrane with water on either side, yes?  That's a layered system.

But frankly, at this point I don't follow at all what you're trying to do.

-Justin




2. It is my understanding that only pullx and pullf files are required for

WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files?
May
I just clean those up in my script, or will they be needed at any point?








Might be useful for troubleshooting or inspecting the microscopic behavior
that gives rise to the free energy profile.  There's always useful stuff
there; rarely do you only care about just a single number coming out of
WHAM.



Sure. My HDD space is limited this time, hence the question on what's
necessary and what's a useful extra.

Thank you,

Alex






--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] Umbrella sampling and PMF calculations

[Alex]

>
>
>>
> Your situation is completely different.  Look into the cylinder settings
> for dealing with a layered system, but I have no experience with them.  To
> be clear - you always need two groups to define the vector (reaction
> coordinate) along which the bias is applied.  So you need to define a
> second group; you can't just say "I'm biasing an ion and that's it."


Okay, I see. However, I have a pretty simple situation: an ion and the rest
of the system, i.e. a membrane with all the atoms it contains, water, and a
counterion to the ion of interest -- which could be the groups in question,
after I use make_ndx properly. The simulations that result in the
pullf/pullx data of interest are using "pseudo" pull, because your pulling
rate is set to zero, so in terms of moving things, nothing actually gets
pulled and this is merely a way of obtaining the pullf data in the
direction of the bias. It sounds like there is little difference between
our systems. My topology of the ion of interest has no restraint in the
Z-direction, i.e. indeed a cylinder type of constraint in-plane. So, when
you say that my situation is completely different, what do you mean? There
is really nothing "layered" about my system...


> 2. It is my understanding that only pullx and pullf files are required for
>> WHAM, along with the tpr's for each of the MD runs, at least that's what
>> follows from the tutorial. Anything about trajectories or energy files?
>> May
>> I just clean those up in my script, or will they be needed at any point?
>>
>>
>


> Might be useful for troubleshooting or inspecting the microscopic behavior
> that gives rise to the free energy profile.  There's always useful stuff
> there; rarely do you only care about just a single number coming out of
> WHAM.
>
>
Sure. My HDD space is limited this time, hence the question on what's
necessary and what's a useful extra.

Thank you,

Alex


>
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Re: [gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/1/17 4:28 PM, Alex wrote:

Just a few quick questions for Justin.

I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

1. In your example, you have two pull groups. My understanding is that both
are pulled relative to each other. In my case, the only thing that's pulled
to create the series of configurations required for WHAM is a single ion,
which is pulled relative to the rest of the system (nothing but a hydrated
membrane with a particular type of hole inside of it). The ion starts above
the hole, enters the hole, then leaves it, the aim here is to find the free
energy associated with sitting in that hole.
I recall (maybe incorrectly) that pull code has some quirks, so will your
procedure work, or is there anything I should be aware of?



Your situation is completely different.  Look into the cylinder settings for 
dealing with a layered system, but I have no experience with them.  To be clear 
- you always need two groups to define the vector (reaction coordinate) along 
which the bias is applied.  So you need to define a second group; you can't just 
say "I'm biasing an ion and that's it."



2. It is my understanding that only pullx and pullf files are required for
WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files? May
I just clean those up in my script, or will they be needed at any point?



Might be useful for troubleshooting or inspecting the microscopic behavior that 
gives rise to the free energy profile.  There's always useful stuff there; 
rarely do you only care about just a single number coming out of WHAM.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling and PMF calculations

[Alex]

Just a few quick questions for Justin.

I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

1. In your example, you have two pull groups. My understanding is that both
are pulled relative to each other. In my case, the only thing that's pulled
to create the series of configurations required for WHAM is a single ion,
which is pulled relative to the rest of the system (nothing but a hydrated
membrane with a particular type of hole inside of it). The ion starts above
the hole, enters the hole, then leaves it, the aim here is to find the free
energy associated with sitting in that hole.
I recall (maybe incorrectly) that pull code has some quirks, so will your
procedure work, or is there anything I should be aware of?

2. It is my understanding that only pullx and pullf files are required for
WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files? May
I just clean those up in my script, or will they be needed at any point?

Thank you,

Alex
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[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,


I want to perfom NVT equilibration, pull code (using pull-geometry = 
direction-periodic)


Prior to this step, energy minimization (500 steps) and NPT equilibration 
(5 steps) was done


As I am new to gromacs and simulations, can anyone tell me whether the 
following NVT code is correct?


Is this code for NVT correct?


title = Umbrella pulling simulation
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 5 ; 100 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc_grps = Protein Non-Protein
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is off
Pcoupl = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no ;

; Pull code

..
..
.


Thanks,
Subashini.K

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Re: [gmx-users] UMBRELLA SAMPLING

[Justin Lemkul]

On 3/4/17 9:24 AM, Subashini .K wrote:

Hi gromacs users,


I want to calculate delta G for protein ligand binding.


Had run the umbrella pulling simulation   for 100 ps (protein ligand solvated 
in water), applying restraint in the protein (using the code in gromacs 
tutorial website, Bevenlab).


But, after running the perl script  (perl distances.pl), did not obtain any 
distance on the right column (summary_distances.dat). It was blank.



(1) Had applied the position restrain of the protein during NPT equilibration.

(2) During puling simulation, again applied the restrain on the protein. Is it 
correct?


How to rectify the mistake and proceed in the right direction?



The script from the tutorial is designed for use with the tutorial and therefore 
makes assumptions about the groups that are in the index file.  Invoke gmx 
distance yourself so you can see how to properly use it, then adjust the script 
as needed.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,


I want to calculate delta G for protein ligand binding.


Had run the umbrella pulling simulation   for 100 ps (protein ligand solvated 
in water), applying restraint in the protein (using the code in gromacs 
tutorial website, Bevenlab).


But, after running the perl script  (perl distances.pl), did not obtain any 
distance on the right column (summary_distances.dat). It was blank.



(1) Had applied the position restrain of the protein during NPT equilibration.

(2) During puling simulation, again applied the restrain on the protein. Is it 
correct?


How to rectify the mistake and proceed in the right direction?



Thanks,

Subashini.K
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[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,



I want to calculate the binding energy (ΔGbind) using umbrella sampling method 
(between protein and ligand which is solvated in water)


How to custom index groups for the pulling simulation?


The protein under consideration has only one chain A.


Thanks,

Subashini.K

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[gmx-users] umbrella sampling pulling direction

[Nikhil Maroli]

Dear all,

My ligand is somewhat inside the protein and im confused in which direction
i should pull the ligand for umbrella sampling. I have attached the *.gro
file.

In my previous US systems ligand was on the 'surface of the protein' so
that it was easy to pull on y or z- direction.

https://goo.gl/qDXojD

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Nikhil Maroli
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Re: [gmx-users] umbrella sampling distances

[Justin Lemkul]

On 11/17/16 10:06 PM, Irem Altan wrote:

Hi,

I’m trying to apply umbrella sampling to a system following Justin Lemkul’s 
tutorial. I’m confused about how the distances are calculated, however. When I 
run a pull simulation and calculate center of mass distances with gmx distance, 
I see that the distance in the 0th configuration is 3.003 nm. When I look at 
the output PMF generated with gmx wham, the PMF starts from 2.56 nm. What could 
I be missing?



Your sampling includes distances as low as 2.56 nm.  This isn't necessarily 
wrong.  The average in the window should match the average calculated by gmx 
distance, but without seeing a whole lot of steps that you left out in your 
description, it's impossible to know if your setup is exactly what you think it 
is.  Confirm the reference distance that grompp prints out before the run, 
consider the strength of the spring constant for the restraint, etc.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] umbrella sampling distances

[Irem Altan]

Hi,

I’m trying to apply umbrella sampling to a system following Justin Lemkul’s 
tutorial. I’m confused about how the distances are calculated, however. When I 
run a pull simulation and calculate center of mass distances with gmx distance, 
I see that the distance in the 0th configuration is 3.003 nm. When I look at 
the output PMF generated with gmx wham, the PMF starts from 2.56 nm. What could 
I be missing?

Best,
Irem
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Re: [gmx-users] Umbrella Sampling

[gozde ergin]

Hey,

Did you change the number inside the distances.pl script?
If you have 1000 files, you need to change the number of 500 on line 6, 13 , 
and  36 (lines start with for loop) make them 1000.
> On 13 Nov 2016, at 11:10, Mouri Ahmed  wrote:
> 
> Hi everyone,
> 
> I have run pulling simulation for the protein complex system. I have got
> 1000 configuration files. And in the summary_distances.dat, I have found
> 0-500 distances.
> 
> How will I select configuration file for the npt_umbrella simulation.
> 
> Thanks in advance. I will be very grateful for the help.
> 
> Best Regards
> Mouri
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[gmx-users] Umbrella Sampling

[Mouri Ahmed]

Hi everyone,

I have run pulling simulation for the protein complex system. I have got
1000 configuration files. And in the summary_distances.dat, I have found
0-500 distances.

How will I select configuration file for the npt_umbrella simulation.

Thanks in advance. I will be very grateful for the help.

Best Regards
Mouri
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[gmx-users] Umbrella Sampling - LINCS error when pull group is in vapor phase

[Dan Gil]

Hi,

I am trying to calculate the adsorption free energy of a molecule onto
water. I want to use umbrella sampling to obtain the free energy profile as
a function of distance normal to a water surface.

I am getting LINCS error when my molecule is in the vapor phase. The error
messages indicate large deviations from the constraints only with the
molecule of interest, and nothing from the waters.

I am using all-bonds constraints.

How should I resolve this problem?

Best Regards,

Dan
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Re: [gmx-users] Umbrella sampling tutorial WHAM issue

[Justin Lemkul]

On 11/10/16 10:46 AM, Lindsay, Richard J. wrote:

Hi,

I am attempting to follow the gromacs umbrella sampling tutorial but have run 
into an issue at the data analysis step.

When I run the gmx wham command I get only one histogram, even though I 
collected 24 umbrella trajectories.



You're probably just plotting it wrong.  xmgrace -nxy histo.xvg, not xmgrace 
histo.xvg.


-Justin


Here is the command I am running:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal

The *-files.dat files each contain a list of the 24 relevant files as such:

pullf-files.dat:

pullf-umbrella0.xvg
...
...
pullf-umbrella23.xvg


tpr-files.dat:
umbrella0.tpr
...
...
umbrella23.tpr


When I run the analysis on one .tpr/.xvg file at a time and run the analysis 24 
times I am able to combine the histograms produced to get the expected result: 
24 well-spaced histograms with reasonable overlap. However I would like to know 
why I am unable to get this result by running gmx wham once as in the tutorial. 
I am using gromacs 5.1.2.


Here is the log file from my original attempt at the wham analysis:

--

Note: Will use 32 OpenMP threads.

Found 24 tpr and 24 pull force files in tpr-files.dat and pullf-files.dat, 
respectively
Reading 12 tpr and pullf files
Automatic determination of boundaries...
File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 
dimensions)
Pull group coordinates not expected in pullx files.
crd 0) k = 1000   position = 0.489812
Use option -v to see this output for all input tpr files

Reading pull force file with pull geometry distance and 1 pull dimensions
Expecting these columns in pull file:
0 reference columns for each individual pull coordinate
1 data columns for each pull coordinate
With 1 pull groups, expect 2 columns (including the time column)

Determined boundaries to 0.445155 and 5.253408

Wrote histo.xvg
Getting initial potential by integration.
Initialized rapid wham stuff (contrib tolerance 4.16667e-08)
Evaluating only 1013 of 4800 expressions.

   1) Maximum change 5.820592e-01
 100) Maximum change 6.205472e-03
 200) Maximum change 1.677333e-03
 300) Maximum change 1.011720e-03
 400) Maximum change 6.767362e-04
 500) Maximum change 5.057361e-04
 600) Maximum change 3.887035e-04
 700) Maximum change 3.053506e-04
 800) Maximum change 2.443217e-04
 900) Maximum change 1.986103e-04
1000) Maximum change 1.689707e-04
1100) Maximum change 1.467826e-04
1200) Maximum change 1.293663e-04
1300) Maximum change 1.141341e-04
1400) Maximum change 1.008461e-04
1500) Maximum change 8.925561e-05
1600) Maximum change 7.913347e-05
1700) Maximum change 7.036949e-05
1800) Maximum change 6.276724e-05
1900) Maximum change 5.603027e-05
2000) Maximum change 5.005392e-05
2100) Maximum change 4.474645e-05
2200) Maximum change 4.119858e-05
2300) Maximum change 3.794030e-05
2400) Maximum change 3.486749e-05
2500) Maximum change 3.199419e-05
2600) Maximum change 2.932535e-05
2700) Maximum change 2.685949e-05
2800) Maximum change 2.459074e-05
2900) Maximum change 2.251030e-05
3000) Maximum change 2.060762e-05
3100) Maximum change 1.887118e-05
3200) Maximum change 1.728904e-05
3300) Maximum change 1.584933e-05
3400) Maximum change 1.454045e-05
3500) Maximum change 1.335133e-05
3600) Maximum change 1.227147e-05
3700) Maximum change 1.129108e-05
3800) Maximum change 1.040106e-05
3900) Maximum change 9.593003e-06
4000) Maximum change 8.859203e-06
4100) Maximum change 8.192607e-06
4200) Maximum change 7.586786e-06
4300) Maximum change 7.035893e-06
4400) Maximum change 6.534625e-06
4500) Maximum change 6.078177e-06
4600) Maximum change 5.662203e-06
4700) Maximum change 5.282778e-06
4800) Maximum change 4.936358e-06
4900) Maximum change 4.619747e-06
5000) Maximum change 4.330065e-06
5100) Maximum change 4.064716e-06
5200) Maximum change 3.821363e-06
5300) Maximum change 3.597901e-06
5400) Maximum change 3.392435e-06
5500) Maximum change 3.203261e-06
5600) Maximum change 3.028843e-06
5700) Maximum change 2.867799e-06
5800) Maximum change 2.718886e-06
5900) Maximum change 2.580983e-06
6000) Maximum change 2.453083e-06
6100) Maximum change 2.334276e-06
6200) Maximum change 2.223746e-06
6300) Maximum change 2.120755e-06
6400) Maximum change 2.024637e-06
6500) Maximum change 1.934795e-06
6600) 

[gmx-users] Umbrella sampling tutorial WHAM issue

[Lindsay, Richard J.]

Hi,

I am attempting to follow the gromacs umbrella sampling tutorial but have run 
into an issue at the data analysis step.

When I run the gmx wham command I get only one histogram, even though I 
collected 24 umbrella trajectories.

Here is the command I am running:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal

The *-files.dat files each contain a list of the 24 relevant files as such:

pullf-files.dat:

pullf-umbrella0.xvg
...
...
pullf-umbrella23.xvg


tpr-files.dat:
umbrella0.tpr
...
...
umbrella23.tpr


When I run the analysis on one .tpr/.xvg file at a time and run the analysis 24 
times I am able to combine the histograms produced to get the expected result: 
24 well-spaced histograms with reasonable overlap. However I would like to know 
why I am unable to get this result by running gmx wham once as in the tutorial. 
I am using gromacs 5.1.2.


Here is the log file from my original attempt at the wham analysis:

--

Note: Will use 32 OpenMP threads.

Found 24 tpr and 24 pull force files in tpr-files.dat and pullf-files.dat, 
respectively
Reading 12 tpr and pullf files
Automatic determination of boundaries...
File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 
dimensions)
Pull group coordinates not expected in pullx files.
crd 0) k = 1000   position = 0.489812
Use option -v to see this output for all input tpr files

Reading pull force file with pull geometry distance and 1 pull dimensions
Expecting these columns in pull file:
0 reference columns for each individual pull coordinate
1 data columns for each pull coordinate
With 1 pull groups, expect 2 columns (including the time column)

Determined boundaries to 0.445155 and 5.253408

Wrote histo.xvg
Getting initial potential by integration.
Initialized rapid wham stuff (contrib tolerance 4.16667e-08)
Evaluating only 1013 of 4800 expressions.

   1) Maximum change 5.820592e-01
 100) Maximum change 6.205472e-03
 200) Maximum change 1.677333e-03
 300) Maximum change 1.011720e-03
 400) Maximum change 6.767362e-04
 500) Maximum change 5.057361e-04
 600) Maximum change 3.887035e-04
 700) Maximum change 3.053506e-04
 800) Maximum change 2.443217e-04
 900) Maximum change 1.986103e-04
1000) Maximum change 1.689707e-04
1100) Maximum change 1.467826e-04
1200) Maximum change 1.293663e-04
1300) Maximum change 1.141341e-04
1400) Maximum change 1.008461e-04
1500) Maximum change 8.925561e-05
1600) Maximum change 7.913347e-05
1700) Maximum change 7.036949e-05
1800) Maximum change 6.276724e-05
1900) Maximum change 5.603027e-05
2000) Maximum change 5.005392e-05
2100) Maximum change 4.474645e-05
2200) Maximum change 4.119858e-05
2300) Maximum change 3.794030e-05
2400) Maximum change 3.486749e-05
2500) Maximum change 3.199419e-05
2600) Maximum change 2.932535e-05
2700) Maximum change 2.685949e-05
2800) Maximum change 2.459074e-05
2900) Maximum change 2.251030e-05
3000) Maximum change 2.060762e-05
3100) Maximum change 1.887118e-05
3200) Maximum change 1.728904e-05
3300) Maximum change 1.584933e-05
3400) Maximum change 1.454045e-05
3500) Maximum change 1.335133e-05
3600) Maximum change 1.227147e-05
3700) Maximum change 1.129108e-05
3800) Maximum change 1.040106e-05
3900) Maximum change 9.593003e-06
4000) Maximum change 8.859203e-06
4100) Maximum change 8.192607e-06
4200) Maximum change 7.586786e-06
4300) Maximum change 7.035893e-06
4400) Maximum change 6.534625e-06
4500) Maximum change 6.078177e-06
4600) Maximum change 5.662203e-06
4700) Maximum change 5.282778e-06
4800) Maximum change 4.936358e-06
4900) Maximum change 4.619747e-06
5000) Maximum change 4.330065e-06
5100) Maximum change 4.064716e-06
5200) Maximum change 3.821363e-06
5300) Maximum change 3.597901e-06
5400) Maximum change 3.392435e-06
5500) Maximum change 3.203261e-06
5600) Maximum change 3.028843e-06
5700) Maximum change 2.867799e-06
5800) Maximum change 2.718886e-06
5900) Maximum change 2.580983e-06
6000) Maximum change 2.453083e-06
6100) Maximum change 2.334276e-06
6200) Maximum change 2.223746e-06
6300) Maximum change 2.120755e-06
6400) Maximum change 2.024637e-06
6500) Maximum change 1.934795e-06
6600) Maximum change 1.850688e-06
6700) Maximum change 1.771827e-06
6800) Maximum change 1.697773e-06
6900) Maximum change 1.628127e-06

Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 11/6/16 1:53 AM, m g wrote:

Dear Justin,
In umbrella sampling tutorial, what force constant was used during the umbrella 
sampling simulations?



Please read the contents of the .mdp files provided in the tutorial.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling

[m g]

Dear Justin,
In umbrella sampling tutorial, what force constant was used during the umbrella 
sampling simulations?

Many thanks,

Mr. Ganj
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Re: [gmx-users] Umbrella sampling tutorial

[gozde ergin]

Any idea on this topic?

Thanks
> On 07 Oct 2016, at 14:13, gozde ergin  wrote:
> 
> Thanks Justin.
> I want infinite dilute bulk that’s why I do not want any surfactant molecule 
> inside the bulk.
> I may put a ‘’wall’’ just below the surface molecules in order to inhibit 
> their travel to bulk but I do not know how to remove this effect from PMF.
> 
> 
>> On 07 Oct 2016, at 13:40, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 10/7/16 4:41 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I would like to ask a question about Justin’s tutorial. By using the
>>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>>> effect of this restraint removed during the WHAM?
>>> 
>> 
>> Not to my knowledge, no.  The restraints in the tutorial are there to mimic 
>> the fact that there are only five peptides, when in reality, there are 
>> millions, so the effects of the forces are quite different in vitro/in vivo. 
>>  Restraining one peptide makes the remaining four peptides more stable, more 
>> realistic.  WHAM doesn't do anything to change this.
>> 
>>> I want to do a similar thing by applying restraint force on the organic
>>> molecule on the bulk water in order to inhibit their movement inside the
>>> bulk. Should I consider the removing of the restraint in PMF?
>>> 
>> 
>> In the case of freely diffusing molecules, I suspect such a restraint would 
>> have a much more profound impact.  Why do you want to do this?
>> 
>> -Justin
>> 
>> -- 
>> ==
>> 
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> 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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>> mail to gmx-users-requ...@gromacs.org.
> 

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Re: [gmx-users] Umbrella sampling tutorial

[gozde ergin]

Thanks Justin.
I want infinite dilute bulk that’s why I do not want any surfactant molecule 
inside the bulk.
I may put a ‘’wall’’ just below the surface molecules in order to inhibit their 
travel to bulk but I do not know how to remove this effect from PMF.


> On 07 Oct 2016, at 13:40, Justin Lemkul  wrote:
> 
> 
> 
> On 10/7/16 4:41 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I would like to ask a question about Justin’s tutorial. By using the
>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>> effect of this restraint removed during the WHAM?
>> 
> 
> Not to my knowledge, no.  The restraints in the tutorial are there to mimic 
> the fact that there are only five peptides, when in reality, there are 
> millions, so the effects of the forces are quite different in vitro/in vivo.  
> Restraining one peptide makes the remaining four peptides more stable, more 
> realistic.  WHAM doesn't do anything to change this.
> 
>> I want to do a similar thing by applying restraint force on the organic
>> molecule on the bulk water in order to inhibit their movement inside the
>> bulk. Should I consider the removing of the restraint in PMF?
>> 
> 
> In the case of freely diffusing molecules, I suspect such a restraint would 
> have a much more profound impact.  Why do you want to do this?
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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] Umbrella sampling tutorial

[Justin Lemkul]

On 10/7/16 4:41 AM, gozde ergin wrote:

Dear all,

I would like to ask a question about Justin’s tutorial. By using the
POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
effect of this restraint removed during the WHAM?



Not to my knowledge, no.  The restraints in the tutorial are there to mimic the 
fact that there are only five peptides, when in reality, there are millions, so 
the effects of the forces are quite different in vitro/in vivo.  Restraining one 
peptide makes the remaining four peptides more stable, more realistic.  WHAM 
doesn't do anything to change this.



I want to do a similar thing by applying restraint force on the organic
molecule on the bulk water in order to inhibit their movement inside the
bulk. Should I consider the removing of the restraint in PMF?



In the case of freely diffusing molecules, I suspect such a restraint would have 
a much more profound impact.  Why do you want to do this?


-Justin

--
==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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[gmx-users] Umbrella sampling tutorial

[gozde ergin]

Dear all,

I would like to ask a question about Justin’s tutorial.
By using the POSRES_B, a restraint is applied on chain B in order to immobile 
it. Is the effect of this restraint removed during the WHAM? 

I want to do a similar thing by applying restraint force on the organic 
molecule on the bulk water in order to inhibit their movement inside the bulk. 
Should I consider the removing of the restraint in PMF?

Thanks in advance.
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Re: [gmx-users] Umbrella sampling

[Justin Lemkul]

On 9/5/16 3:16 AM, masoud aliyar wrote:

Hi everybody
I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything
is ok but some aspects of the procedure remain a bit unclear to me. Why
don’t we need to do NVT equilibration before first MD? And why pull codes


Equilibrate however you like.  There is no one-size-fits-all method.

In this case, I don't think there is much value in an additional NVT simulation 
because the starting snapshots are from a previous dynamics run (the SMD).



are applied during NPT equilibration of selected windows or extracted
frames?


Apply the conditions you would during simulation.  You can restrain via normal 
position restraints, but those allow deviations in the initial absolute 
positions.  If those allow sufficient variation, then the pull code has to do a 
large amount of work in the initial time steps, which can be unstable or 
otherwise undo some of the work of equilibration.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling

[masoud aliyar]

Hi everybody
I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything
is ok but some aspects of the procedure remain a bit unclear to me. Why
don’t we need to do NVT equilibration before first MD? And why pull codes
are applied during NPT equilibration of selected windows or extracted
frames?
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Re: [gmx-users] umbrella sampling pull to -z direction

[Justin Lemkul]

On 8/19/16 9:32 AM, Nikhil Maroli wrote:

Dear Justin,
Thanks for your answer,
I tried with
pull_coord1_rate = -0.01

but its not working ,the ligand is going 'inside' the protein
I have tried with

pull_coord1_geometry= direction

*pull-coord1-vec   = 0 0 -1*


*still same results*


*Could you tell me where im wrong?*



This suggests your setup/convention is wrong.  So your purpose is to pull a 
ligand away from a protein?  If the above is pulling them closer, then do the 
opposite.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] umbrella sampling pull to -z direction

[Nikhil Maroli]

Dear Justin,
Thanks for your answer,
I tried with
pull_coord1_rate = -0.01

but its not working ,the ligand is going 'inside' the protein
I have tried with

pull_coord1_geometry= direction

*pull-coord1-vec   = 0 0 -1*


*still same results*


*Could you tell me where im wrong?*
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Re: [gmx-users] umbrella sampling pull to -z direction

[Justin Lemkul]

On 8/19/16 7:59 AM, Nikhil Maroli wrote:

Dear all,
I wanted to do an US of a protein-ligand system, my ligand is situated on
-z direction as in Fig (below link)


if I change the option

pull_coord1_dim = N N Y


to

pull_coord1_dim = N N -Y


it will work or is ther any way to deal in this situations?



There is no such option as -Y.  N = no, Y = yes.

To pull along a negative direction, either specify a negative axis for pulling 
or supply a negative pull rate, depending on which geometry you're using.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] umbrella sampling pull to -z direction

[Nikhil Maroli]

Dear all,
I wanted to do an US of a protein-ligand system, my ligand is situated on
-z direction as in Fig (below link)


if I change the option

pull_coord1_dim = N N Y


to

pull_coord1_dim = N N -Y


it will work or is ther any way to deal in this situations?


https://drive.google.com/file/d/0BxaQk_pcR9viQ3hiWkNXNGZSbzg/view?usp=sharing


Thanks
-- 
Regards,
Nikhil Maroli
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Re: [gmx-users] umbrella sampling for determining interfacial energy

[Ray Chao]

Thank you very much.​
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Re: [gmx-users] umbrella sampling for determining interfacial energy

[Dan Gil]

Hi, this is a good coincidence, but I think I do something very similar to
what you just described.

I use umbrella sampling to estimate the free energy profile as a function
of distance from a liquid-vapor interface. Then, the free energy cost of
adsorption to the interface can be approximated. I can imagine that it
should work just as well with liquid-solid interfaces.

I found these references helpful.

A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
 http://dx.doi.org/10.1103/PhysRevLett.63.1195
- P.-C. Li and D. E. Makarov, J. Phys. Chem. B 108, 745 (2004).
 http://dx.doi.org/10.1021/jp0363895

On Thu, Aug 11, 2016 at 2:58 PM, Ray Chao  wrote:

> Hi, gmx users,
>
> I am doing research on liquid-solid interface. I see that the umbrella
> sampling can be used to calculate the binding energy, so I am wondering if
> the umbrella sampling can be used to calculate the interfacial free energy
> between different liquids and solids by pulling the liquid towards the
> solid surface. If not, is there any other way to do this in Gromacs?
>
> Thank you very much.
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Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

[Nikhil Maroli]

Hi 

already it is answered.

run the gmx distance command to understand the problem.

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Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

[amitbehra]

Hello all,
I was practicing the umbrella sampling tutorial by Dr. Justin Lemkul. In
my summary_distances.dat file there is only one column ( the column for
centre of mass is missing ).

Can anyone say what possible mistakes I must have done.

Regards,
Amit Behera
Dept. of Chemical Engg.,
IISc, India
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Re: [gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

[Justin Lemkul]

On 6/7/16 3:13 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello,
I was running the simulation for the umbrella sampling tutorial by Dr.
Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they
were mentioned.
But in my summary_distances.dat there is one column. the COM column is
missing. I am new to gromacs . So please help me out.



That means the gmx distance commands failed.  Run one interactively to see what 
error you get.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

[amitbehra]

Hello,
I was running the simulation for the umbrella sampling tutorial by Dr.
Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they
were mentioned.
But in my summary_distances.dat there is one column. the COM column is
missing. I am new to gromacs . So please help me out.

Regards,

Amit Behera,
Dept. of Chemical Engineering,
Indian Institute of Science, Bengaluru,
India.


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[gmx-users] Umbrella Sampling - choice of pull-coord?-dim

[Lukas Zimmermann]

Dear GROMACS users,

I am interested in the role of the mdp parameter pull-coord?-dim when
sampling
a particular umbrella window after having generated initial configurations
for, say, the
COM distance between two groups being the reaction coordinate.

I know that these options can be controlled to restrict the actual pulling,
say with geometry distance,  to a subset of the pull vector components, for
instance to enable
aligment of the pull vector with the box dimensions.

However, I do not understand its role when performing umbrella sampling
along the reaction coordinate.
I know that the pull-code then controls the COM distance between the pull
groups with a (usually) harmonic potential, but what effect will
pull-coord?-dim have?

I observe different behavior for my toy system consisting of two methanol
molecules in vacuum.
With all components enables, I need to correct the PMF for entropic
decrease in the PMF,
since the methanol is sampled on a sphere with increasing radius.
If only allowing one component, the PMF will be flat, but different values
for delta G
result.

Also, in the US Tutorial by Justin, the US code uses:

pull_coord1_dim = N N Y

Is there any particular reason, not to set

pull_coord1_dim = Y Y Y

here? Would this setting also be justified? Since, as far as I understood
the procedure,  pulling

is just there for generating the initial configurations and US is more or
less independent of this.



Many thanks in advance!

Lukas
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Re: [gmx-users] Umbrella sampling version 5.0

[Justin Lemkul]

On 5/3/16 9:18 PM, Steve Seibold wrote:

I have used the older version of Gromacs 4.x.x to do umbrella sampling; I have 
just installed Gromacs 5.0 and found that the tutorials on line are now for 
Gromacs 5.1. Is there a huge difference in the protocol from 5.0 to 5.1? I used 
a youtube illustration to install Gromacs. I tried to install 5.1.x but it 
failed...If necessary I will attempt to install 5.1.x, but only if it is 
necessary


The pull code underwent significant changes between 4.6.x to 5.0.x to 5.1.x, so 
I never did a 5.0 tutorial because I knew it was going to be completely changed 
later.


Installing 5.0 and 5.1 should be basically identical processes.  There's no real 
reason to start new science with old software :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling version 5.0

[Steve Seibold]

I have used the older version of Gromacs 4.x.x to do umbrella sampling; I have 
just installed Gromacs 5.0 and found that the tutorials on line are now for 
Gromacs 5.1. Is there a huge difference in the protocol from 5.0 to 5.1? I used 
a youtube illustration to install Gromacs. I tried to install 5.1.x but it 
failed...If necessary I will attempt to install 5.1.x, but only if it is 
necessary
thanks, Steve
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[gmx-users] Umbrella sampling without pull

[Sana Saeed]

Himy question is , can we use Umbrella Sampling without Pulling, Is it 
possible? i know the concept of Umbrella sampling and Replica Exchange, i have 
performed solvation of different small molecules in water and calculated 
energies. some of results are not good, so how can i improve these results, 
with simple solvation which method can be performed , US or replica exchange. 
Thanks in advance
Sana Saeed Khan,Research AssistantChemoinformatics LabGraduate Student, MS 
bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.
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Re: [gmx-users] Umbrella sampling along PCA eigenvector using make_edi

[Kutzner, Carsten]

Dear Hendrik,

that indeed looks a bit strange. If you provide the necessary input
files for a test, I could have a look at what might be wrong.
You can put them somewhere for download or email them directly
to me (not to the list, they will not be accepted).

Carsten


> On 30 Mar 2016, at 16:11, Hendrik Goeddeke  wrote:
> 
> Hi everyone,
> 
> I want to do umbrella sampling along a PCA eigenvector using 'gmx
> make_edi'. The eigenvectors of the protein backbone atoms were computed
> using 'gmx covar'. The command for generating the 'sam.edi' file looks
> like the following:
> 
> gmx make_edi -s topol.tpr -f eigenvec.trr -eig eigenval.xvg -restrain
> yes -harmonic yes -ori window1_backbone.gro -flood 1 -tau 0 -Eflnull 1000
> 
> The file 'window1_backbone.gro' just contains the backbone atoms of a
> snapshot called 'window1.gro', which was used for generating
> 'topol.tpr'. I changed the eigenvalue of the first eigenvector in
> 'eigenval.xvg' to 1 to get a force constant of 1000 kJ/(mol*nm^2). When
> I then start 'gmx mdrun -ei sam.edi' the output states that the initial
> RMSD from the reference structure is not zero:
> 
> ...
> ED: Flooding 1 eigenvector.
> ED: Initial RMSD from reference after fit = 0.371082 nm
> ...
> 
> But when I compute the RMSD to the reference structure ('topol.tpr')
> manually by using 'gmx rms', the RMSD is zero as expected. This excludes
> a possibly wrong PBC representaion of the ED group (backbone atoms). I
> looked at the code ('edsam.c') but it seems that the RMSD is also
> computed from 'topol.tpr', which was specified in 'gmx make_edi'. I
> repeated the procedure many times but could not find any mistake.
> 
> Any help is highly appreciated.
> 
> Thank you very much in advance!
> 
> All the best,
> Hendrik
> 
> 
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[gmx-users] Umbrella sampling along PCA eigenvector using make_edi

[Hendrik Goeddeke]

Hi everyone,

I want to do umbrella sampling along a PCA eigenvector using 'gmx
make_edi'. The eigenvectors of the protein backbone atoms were computed
using 'gmx covar'. The command for generating the 'sam.edi' file looks
like the following:

gmx make_edi -s topol.tpr -f eigenvec.trr -eig eigenval.xvg -restrain
yes -harmonic yes -ori window1_backbone.gro -flood 1 -tau 0 -Eflnull 1000

The file 'window1_backbone.gro' just contains the backbone atoms of a
snapshot called 'window1.gro', which was used for generating
'topol.tpr'. I changed the eigenvalue of the first eigenvector in
'eigenval.xvg' to 1 to get a force constant of 1000 kJ/(mol*nm^2). When
I then start 'gmx mdrun -ei sam.edi' the output states that the initial
RMSD from the reference structure is not zero:

...
ED: Flooding 1 eigenvector.
ED: Initial RMSD from reference after fit = 0.371082 nm
...

But when I compute the RMSD to the reference structure ('topol.tpr')
manually by using 'gmx rms', the RMSD is zero as expected. This excludes
a possibly wrong PBC representaion of the ED group (backbone atoms). I
looked at the code ('edsam.c') but it seems that the RMSD is also
computed from 'topol.tpr', which was specified in 'gmx make_edi'. I
repeated the procedure many times but could not find any mistake.

Any help is highly appreciated.

Thank you very much in advance!

All the best,
Hendrik


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Re: [gmx-users] Umbrella sampling error with drug molecule

[Justin Lemkul]

On 3/1/16 7:59 PM, Khuong Truong Gia wrote:

Hi all,


I am using gromacs to run umbrella sampling simulation with a drug molecule
(polymer). I got force field from PRODRG.
When run pulling the drug I got this error:

step 86530014: Water molecule starting at atom 8336 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 49 and 59
at distance 3.355 which is larger than the table limit 2.076 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 86530015, time 173060 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 14.609595, max 619.843628 (between atoms 46 and 47)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
   4  5   90.00.1056   0.1073  0.1000
  18 19   32.40.1495   0.1588  0.1440
  20 21   50.70.1444   0.1265  0.1520
  20 28   32.70.1429   0.1885  0.1440
  ...
It's seem that the drug molecule is very flexible and it makes the system
blowing up. Is it right?


Not likely.  A sound topology should run stably as long as all the other 
settings are sensible.  But PRODRG topologies are of inadequate quality for any 
reliable simulation, so you need to optimize it.


Then follow the normal troubleshooting advice.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella sampling error with drug molecule

[Khuong Truong Gia]

Hi all,


I am using gromacs to run umbrella sampling simulation with a drug molecule
(polymer). I got force field from PRODRG.
When run pulling the drug I got this error:

step 86530014: Water molecule starting at atom 8336 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 49 and 59
at distance 3.355 which is larger than the table limit 2.076 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 86530015, time 173060 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 14.609595, max 619.843628 (between atoms 46 and 47)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  4  5   90.00.1056   0.1073  0.1000
 18 19   32.40.1495   0.1588  0.1440
 20 21   50.70.1444   0.1265  0.1520
 20 28   32.70.1429   0.1885  0.1440
 ...
It's seem that the drug molecule is very flexible and it makes the system
blowing up. Is it right?
If so, how can I pull a flexible molecule? Please give me some suggestion.
Thanks in advance.

Best regards,
Khuong
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[gmx-users] Umbrella Sampling, Analysis Step

[Misa Banno]

Dear Gromacs users,

I've run the umbrella sampling. I could draw histograms with sufficient 
overlap, so I determined all of the simulations reached enough length of 
time. Now it's the analysis step.


When I chose tpr files and pullf.xvg (forces) files as the input to 
wham, I was able to analyze and draw PMF curve previously.


However, I chose tpr files and pullx.xvg (coordinates) files, I couldn't.
The command line is below.


gmx wham -it tpr-files.dat -ix pullx-files.dat  -o -hist -unit kCal -b 5 -e 
20


I got the profile.xvg but all PMF values are zero in that file.

While running gmx wham, I was getting warnings like below.
Warning, poor sampling bin 199 (z=-1.00185). Check your histograms!

I did simulation by using following COM pulling options:
; COM PULLING
pull = umbrella
pull_geometry= cylinder
pull_dim = N N Y
pull_r1  = 2
pull_r0  = 3
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 100
pull_nstfout = 100
pull_ngroups = 2
pull-ncoords = 1
pull-group1-name = zpopc
pull-group2-name = Protein
pull-coord1-groups   = 1 2
pull-coord1-origin   = 0 0 0
pull-coord1-vec  = 0 0 -1.0
pull-coord1-init = 0
pull-coord1-rate = 0
pull-coord1-k= 1000
pull-coord1-kB   = 0


Please help me in this regard.

Many Thanks
Misa Banno

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[gmx-users] umbrella sampling error

[Nikhil Maroli]

Dear all,
im running umbrella sampling when invoke the following command i got the
follwoing warnings and grompp terminated becasue of so much warning
,initially i neutralised the My protein-Ligand system with NACl,so how come
there will be a charge?  (NOTE 5)what i can do for that?  can i use maxwarn
option as im running equilibration?

  gmx grompp -f npt_umbrella.mdp -c conf128.gro -p topol.top -n index.ndx
-o npt125.tpr


NOTE 1 [file npt_umbrella.mdp, line 66]:
  npt_umbrella.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.




NOTE 2 [file npt_umbrella.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.



NOTE 3 [file npt_umbrella.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 4 [file npt_umbrella.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1


WARNING 1 [file npt_umbrella.mdp]:
  You are generating velocities so I am assuming you are equilibrating a
  system. You are using Parrinello-Rahman pressure coupling, but this can
  be unstable for equilibration. If your system crashes, try equilibrating
  first with Berendsen pressure coupling. If you are not equilibrating the
  system, you can probably ignore this warning.





*NOTE 5 [file topol.top, line 77254]:*
*  System has non-zero total charge: -11.94*
*  Total charge should normally be an integer. See*
*  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
*
*  for discussion on how close it should be to an integer.*




Setting gen_seed to 2839808349
Velocities were taken from a Maxwell distribution at 310 K
Removing all charge groups because cutoff-scheme=Verlet
Pull group 1 'Chain_A' has 8120 atoms
Pull group 2 'Chain_B' has 33 atoms
Number of degrees of freedom in T-Coupling group Protein is 16109.61
Number of degrees of freedom in T-Coupling group non-Protein is 108398.39
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.408 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x56x104, spacing 0.111 0.116 0.116
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1  8120  4060
   233  8137   1.117 nm  1.117 nm
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 32 Mb of data

There were 5 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1
Source code file:
/home/user/gromacs-5.1/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
Too many warnings (1), gmx terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] umbrella sampling error

[Justin Lemkul]

On 1/5/16 5:36 AM, Nikhil Maroli wrote:

Dear all,
im running umbrella sampling when invoke the following command i got the
follwoing warnings and grompp terminated becasue of so much warning
,initially i neutralised the My protein-Ligand system with NACl,so how come
there will be a charge?  (NOTE 5)what i can do for that?  can i use maxwarn
option as im running equilibration?



Well, simply put, you did something wrong because you still have a net charge of 
-12 (ignore the floating-point difference here, it's actually -12).


Don't use -maxwarn to simply overcome something inconvenient, though in this 
case its use has no bearing on any notes and only affects the warning, which you 
should heed; your selected method is not necessarily stable under the conditions 
specified.


-Justin


   gmx grompp -f npt_umbrella.mdp -c conf128.gro -p topol.top -n index.ndx
-o npt125.tpr


NOTE 1 [file npt_umbrella.mdp, line 66]:
   npt_umbrella.mdp did not specify a value for the .mdp option
   "cutoff-scheme". Probably it was first intended for use with GROMACS
   before 4.6. In 4.6, the Verlet scheme was introduced, but the group
   scheme was still the default. The default is now the Verlet scheme, so
   you will observe different behaviour.




NOTE 2 [file npt_umbrella.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.



NOTE 3 [file npt_umbrella.mdp]:
   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
   nstcomm to nstcalcenergy


NOTE 4 [file npt_umbrella.mdp]:
   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1


WARNING 1 [file npt_umbrella.mdp]:
   You are generating velocities so I am assuming you are equilibrating a
   system. You are using Parrinello-Rahman pressure coupling, but this can
   be unstable for equilibration. If your system crashes, try equilibrating
   first with Berendsen pressure coupling. If you are not equilibrating the
   system, you can probably ignore this warning.





*NOTE 5 [file topol.top, line 77254]:*
*  System has non-zero total charge: -11.94*
*  Total charge should normally be an integer. See*
*  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
*
*  for discussion on how close it should be to an integer.*




Setting gen_seed to 2839808349
Velocities were taken from a Maxwell distribution at 310 K
Removing all charge groups because cutoff-scheme=Verlet
Pull group 1 'Chain_A' has 8120 atoms
Pull group 2 'Chain_B' has 33 atoms
Number of degrees of freedom in T-Coupling group Protein is 16109.61
Number of degrees of freedom in T-Coupling group non-Protein is 108398.39
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.408 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x56x104, spacing 0.111 0.116 0.116
Pull group  natoms  pbc atom  distance at start  reference at t=0
1  8120  4060
233  8137   1.117 nm  1.117 nm
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 32 Mb of data

There were 5 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1
Source code file:
/home/user/gromacs-5.1/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
Too many warnings (1), gmx terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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[gmx-users] Umbrella Sampling and GPU

[Nikhil Maroli]

Dear users,
i would like to perform Umbrella sampling on few protein-ligand system,
i wanted to know is it possible to run it in GPU? (Tesla k20)
Thanks
-- 
Ragards,
Nikhil Maroli
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