Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Thank you :)

On 17 August 2016 at 10:57, Justin Lemkul  wrote:

>
>
> On 8/16/16 8:55 PM, Billy Williams-Noonan wrote:
>
>> Justin,
>>
>> Does *gmx distance* plot the distance between the COM of two index groups?
>>
>>
> It will do whatever you specify (examples on gromacs.org) but yes, it
> does exactly this.
>
> -Justin
>
> Billy
>>
>> On 17 August 2016 at 10:50, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 8/16/16 8:28 PM, Billy Williams-Noonan wrote:
>>>
>>> Thank you that is what I have been doing... :)

 My problem is that I don't have the average COM distance for each
 simulation.  Yes I specify what distance I want in the .mdp settings,
 but
 in the earlier umbrella windows our average COM distance deviates
 somewhat
 from the distance set in the mdp settings.  So I need a reliable way of
 getting an average COM distance to match the average energy output from
 gmx
 energy.


 This is the primary function of gmx distance.
>>>
>>> -Justin
>>>
>>>
>>> Best,
>>>

 Billy



 On 17 August 2016 at 00:28, David van der Spoel 
 wrote:

 On 16/08/16 16:02, Billy Williams-Noonan wrote:

>
> Hi David,
>
>>
>> Yes it's a basic question...  More about my inexperience with Gromacs
>> than
>> anything (and maybe my chemistry background, not my math
>> background...)
>>
>> Gmx energy gives an enthalpy against time in the .xvg output, am
>> trying
>> to
>> translate that to enthalpy against pull distance.
>>
>> What I had been doing was taking the mean state from each distribution
>> in
>> the histo.xvg output, matching that up to a corresponding pull
>> distance,
>> and assuming that the mean enthalpy from gmx energy also matched up to
>> that
>> pull distance.
>>
>> Is there a better way?
>>
>> You want to average over all conformations in the simulation, same as
>>
> you
> do in the PMF. So for each distance you compute the average energy with
> gmx
> energy and plot it.
>
>
> Best regards,
>
>>
>> Billy
>> On Tuesday, 16 August 2016, David van der Spoel > >
>> wrote:
>>
>> On 16/08/16 09:28, Billy Williams-Noonan wrote:
>>
>>
>>> Hi David,
>>>
>>>
I was wondering if you had any advice on how to plot enthalpy
 against
 COM pulling distance in the same manner that you have in *Figure 4*
 above?

 Maybe I don't understand the question, but I'd say you just plot the

 potential energy (from the energy file) with error bar for each data
>>> point
>>> and normalize to zero at infinite distance.
>>>
>>>
>>>Best regards,
>>>

 Billy

 On 2 August 2016 at 18:15, Billy Williams-Noonan <
 billy.williams-noo...@monash.edu> wrote:

 Yes we've noticed that.  Our error estimates for enthalpy are quite
 high

 compared to the free energies at each umbrella window.

>
> On 2 August 2016 at 17:10, David van der Spoel <
> sp...@xray.bmc.uu.se
>
>>
>> wrote:
>
> On 20/07/16 02:51, Billy Williams-Noonan wrote:
>
>
> Hi David,
>>
>>
>>   Thank you...!  To clarify, in Figure 4 of the paper referred to,
>>> you
>>> seem
>>> to have plotted the enthalpy of each frame against the COM pull
>>> distance
>>> and then used those values and the PMFs at each point to compute
>>> -TdS ?
>>> If
>>> so I might do something similar.
>>>
>>> Yes indeed.
>>>
>>>
>>> The only problem is that enthalpies converge much more slowly
>> than
>> free
>> energies.
>>
>>
>> Billy
>>
>>
>> On Wednesday, 20 July 2016, David van der Spoel <
>>> sp...@xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 19/07/16 12:22, Billy Williams-Noonan wrote:
>>>
>>>
>>> Hi David,
>>>


   Thank you for all your responses on here. :)  We'll have to
 make

> you
> an
> author if/when this gets published haha.
>
>Will try to use gmx covar / anaeig at every point but my
> system
> has
> 30,000 atoms so it may not be completely faesible to get an
> accurate
> value
> for the system (same problem as before).
>
> You only do this for the biomolecules separately, not the
> water.
>

Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Justin Lemkul]

On 8/16/16 8:55 PM, Billy Williams-Noonan wrote:

Justin,

Does *gmx distance* plot the distance between the COM of two index groups?



It will do whatever you specify (examples on gromacs.org) but yes, it does 
exactly this.


-Justin


Billy

On 17 August 2016 at 10:50, Justin Lemkul  wrote:




On 8/16/16 8:28 PM, Billy Williams-Noonan wrote:


Thank you that is what I have been doing... :)

My problem is that I don't have the average COM distance for each
simulation.  Yes I specify what distance I want in the .mdp settings, but
in the earlier umbrella windows our average COM distance deviates somewhat
from the distance set in the mdp settings.  So I need a reliable way of
getting an average COM distance to match the average energy output from
gmx
energy.



This is the primary function of gmx distance.

-Justin


Best,


Billy



On 17 August 2016 at 00:28, David van der Spoel 
wrote:

On 16/08/16 16:02, Billy Williams-Noonan wrote:


Hi David,


Yes it's a basic question...  More about my inexperience with Gromacs
than
anything (and maybe my chemistry background, not my math background...)

Gmx energy gives an enthalpy against time in the .xvg output, am trying
to
translate that to enthalpy against pull distance.

What I had been doing was taking the mean state from each distribution
in
the histo.xvg output, matching that up to a corresponding pull distance,
and assuming that the mean enthalpy from gmx energy also matched up to
that
pull distance.

Is there a better way?

You want to average over all conformations in the simulation, same as

you
do in the PMF. So for each distance you compute the average energy with
gmx
energy and plot it.


Best regards,


Billy
On Tuesday, 16 August 2016, David van der Spoel 
wrote:

On 16/08/16 09:28, Billy Williams-Noonan wrote:



Hi David,



   I was wondering if you had any advice on how to plot enthalpy
against
COM pulling distance in the same manner that you have in *Figure 4*
above?

Maybe I don't understand the question, but I'd say you just plot the


potential energy (from the energy file) with error bar for each data
point
and normalize to zero at infinite distance.


   Best regards,


Billy

On 2 August 2016 at 18:15, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

Yes we've noticed that.  Our error estimates for enthalpy are quite
high

compared to the free energies at each umbrella window.


On 2 August 2016 at 17:10, David van der Spoel 
wrote:

On 19/07/16 12:22, Billy Williams-Noonan wrote:


Hi David,



  Thank you for all your responses on here. :)  We'll have to make

you
an
author if/when this gets published haha.

   Will try to use gmx covar / anaeig at every point but my
system
has
30,000 atoms so it may not be completely faesible to get an
accurate
value
for the system (same problem as before).

You only do this for the biomolecules separately, not the water.




   Could I simply use gmx energy and get an ensemble average
enthalpy

for

each point?  Then I can use the Gibbs free energy equation to
solve
for
entropy.

Yes, this is what we did in the paper :).




Billy


On Tuesday, 19 July 2016, David van der Spoel <

sp...@xray.bmc.uu.se>
wrote:

On 19/07/16 09:47, Billy Williams-Noonan wrote:


Hi All,




   I have seen papers where enthalpy and entropy are plotted


against
the
distance of a steered MD pull and am wanting to do something
similar.

   I have run a steered MD simulation pulling a cyclic peptide
out
of
the
binding site and the PMF calculation with *gmx wham* was in
reasonable
agreement with experiment.  to

We have published stuff like that (e.g. J. Chem. Theor.
Comput. 9
pp.

4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)

There are two main ways of doing this, rerunning the PMF at

different
temperatures and using the Van 't Hoff equation, or computing
the
entropy
(approximately) using gmx covar / gmx anaeig for each of the
species.

gmx sham is just for plotting an energy landscape, e.g.
J. Mol. Biol. 354 pp. 173-183 (2005)



   What I would like now is plot the entropy and enthalpy
components

against the pull distance.  I stumbled across *gmx sham* and
would

like

to
use that, however I can't find any information on how to use it
online.  I
found these posts on online forums but have found them to be
unhelpful
(I'm
sure it makes sense, it's just I am more of a chemist than a
mathematician).

Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Justin,

Does *gmx distance* plot the distance between the COM of two index groups?

Billy

On 17 August 2016 at 10:50, Justin Lemkul  wrote:

>
>
> On 8/16/16 8:28 PM, Billy Williams-Noonan wrote:
>
>> Thank you that is what I have been doing... :)
>>
>> My problem is that I don't have the average COM distance for each
>> simulation.  Yes I specify what distance I want in the .mdp settings, but
>> in the earlier umbrella windows our average COM distance deviates somewhat
>> from the distance set in the mdp settings.  So I need a reliable way of
>> getting an average COM distance to match the average energy output from
>> gmx
>> energy.
>>
>>
> This is the primary function of gmx distance.
>
> -Justin
>
>
> Best,
>>
>> Billy
>>
>>
>>
>> On 17 August 2016 at 00:28, David van der Spoel 
>> wrote:
>>
>> On 16/08/16 16:02, Billy Williams-Noonan wrote:
>>>
>>> Hi David,

 Yes it's a basic question...  More about my inexperience with Gromacs
 than
 anything (and maybe my chemistry background, not my math background...)

 Gmx energy gives an enthalpy against time in the .xvg output, am trying
 to
 translate that to enthalpy against pull distance.

 What I had been doing was taking the mean state from each distribution
 in
 the histo.xvg output, matching that up to a corresponding pull distance,
 and assuming that the mean enthalpy from gmx energy also matched up to
 that
 pull distance.

 Is there a better way?

 You want to average over all conformations in the simulation, same as
>>> you
>>> do in the PMF. So for each distance you compute the average energy with
>>> gmx
>>> energy and plot it.
>>>
>>>
>>> Best regards,

 Billy
 On Tuesday, 16 August 2016, David van der Spoel 
 wrote:

 On 16/08/16 09:28, Billy Williams-Noonan wrote:

>
> Hi David,
>
>>
>>I was wondering if you had any advice on how to plot enthalpy
>> against
>> COM pulling distance in the same manner that you have in *Figure 4*
>> above?
>>
>> Maybe I don't understand the question, but I'd say you just plot the
>>
> potential energy (from the energy file) with error bar for each data
> point
> and normalize to zero at infinite distance.
>
>
>Best regards,
>>
>> Billy
>>
>> On 2 August 2016 at 18:15, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Yes we've noticed that.  Our error estimates for enthalpy are quite
>> high
>>
>> compared to the free energies at each umbrella window.
>>>
>>> On 2 August 2016 at 17:10, David van der Spoel >> >
>>> wrote:
>>>
>>> On 20/07/16 02:51, Billy Williams-Noonan wrote:
>>>
>>>
 Hi David,


>   Thank you...!  To clarify, in Figure 4 of the paper referred to,
> you
> seem
> to have plotted the enthalpy of each frame against the COM pull
> distance
> and then used those values and the PMFs at each point to compute
> -TdS ?
> If
> so I might do something similar.
>
> Yes indeed.
>
>
 The only problem is that enthalpies converge much more slowly than
 free
 energies.


 Billy


> On Wednesday, 20 July 2016, David van der Spoel <
> sp...@xray.bmc.uu.se>
> wrote:
>
> On 19/07/16 12:22, Billy Williams-Noonan wrote:
>
>
> Hi David,
>>
>>
>>   Thank you for all your responses on here. :)  We'll have to make
>>> you
>>> an
>>> author if/when this gets published haha.
>>>
>>>Will try to use gmx covar / anaeig at every point but my
>>> system
>>> has
>>> 30,000 atoms so it may not be completely faesible to get an
>>> accurate
>>> value
>>> for the system (same problem as before).
>>>
>>> You only do this for the biomolecules separately, not the water.
>>>
>>>
>>>
>>Could I simply use gmx energy and get an ensemble average
>> enthalpy
>>
>> for
>>> each point?  Then I can use the Gibbs free energy equation to
>>> solve
>>> for
>>> entropy.
>>>
>>> Yes, this is what we did in the paper :).
>>>
>>>
>>>
>> Billy
>>
>>
>> On Tuesday, 19 July 2016, David van der Spoel <
>>> sp...@xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 19/07/16 09:47, Billy Williams-Noonan wrote:
>>>
>>>
>>> Hi All,
>>>


I have seen papers where enthalpy and 

Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Justin Lemkul]

On 8/16/16 8:28 PM, Billy Williams-Noonan wrote:

Thank you that is what I have been doing... :)

My problem is that I don't have the average COM distance for each
simulation.  Yes I specify what distance I want in the .mdp settings, but
in the earlier umbrella windows our average COM distance deviates somewhat
from the distance set in the mdp settings.  So I need a reliable way of
getting an average COM distance to match the average energy output from gmx
energy.



This is the primary function of gmx distance.

-Justin


Best,

Billy



On 17 August 2016 at 00:28, David van der Spoel 
wrote:


On 16/08/16 16:02, Billy Williams-Noonan wrote:


Hi David,

Yes it's a basic question...  More about my inexperience with Gromacs than
anything (and maybe my chemistry background, not my math background...)

Gmx energy gives an enthalpy against time in the .xvg output, am trying to
translate that to enthalpy against pull distance.

What I had been doing was taking the mean state from each distribution in
the histo.xvg output, matching that up to a corresponding pull distance,
and assuming that the mean enthalpy from gmx energy also matched up to
that
pull distance.

Is there a better way?


You want to average over all conformations in the simulation, same as you
do in the PMF. So for each distance you compute the average energy with gmx
energy and plot it.



Best regards,

Billy
On Tuesday, 16 August 2016, David van der Spoel 
wrote:

On 16/08/16 09:28, Billy Williams-Noonan wrote:


Hi David,


   I was wondering if you had any advice on how to plot enthalpy against
COM pulling distance in the same manner that you have in *Figure 4*
above?

Maybe I don't understand the question, but I'd say you just plot the

potential energy (from the energy file) with error bar for each data
point
and normalize to zero at infinite distance.



   Best regards,

Billy

On 2 August 2016 at 18:15, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

Yes we've noticed that.  Our error estimates for enthalpy are quite high


compared to the free energies at each umbrella window.

On 2 August 2016 at 17:10, David van der Spoel 
wrote:

On 20/07/16 02:51, Billy Williams-Noonan wrote:



Hi David,



  Thank you...!  To clarify, in Figure 4 of the paper referred to,
you
seem
to have plotted the enthalpy of each frame against the COM pull
distance
and then used those values and the PMFs at each point to compute
-TdS ?
If
so I might do something similar.

Yes indeed.



The only problem is that enthalpies converge much more slowly than
free
energies.


Billy



On Wednesday, 20 July 2016, David van der Spoel <
sp...@xray.bmc.uu.se>
wrote:

On 19/07/16 12:22, Billy Williams-Noonan wrote:



Hi David,



  Thank you for all your responses on here. :)  We'll have to make
you
an
author if/when this gets published haha.

   Will try to use gmx covar / anaeig at every point but my system
has
30,000 atoms so it may not be completely faesible to get an
accurate
value
for the system (same problem as before).

You only do this for the biomolecules separately, not the water.




   Could I simply use gmx energy and get an ensemble average
enthalpy


for
each point?  Then I can use the Gibbs free energy equation to solve
for
entropy.

Yes, this is what we did in the paper :).




Billy



On Tuesday, 19 July 2016, David van der Spoel <
sp...@xray.bmc.uu.se>
wrote:

On 19/07/16 09:47, Billy Williams-Noonan wrote:


Hi All,



   I have seen papers where enthalpy and entropy are plotted

against
the
distance of a steered MD pull and am wanting to do something
similar.

   I have run a steered MD simulation pulling a cyclic peptide
out
of
the
binding site and the PMF calculation with *gmx wham* was in
reasonable
agreement with experiment.  to

We have published stuff like that (e.g. J. Chem. Theor. Comput. 9
pp.

4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)


There are two main ways of doing this, rerunning the PMF at
different
temperatures and using the Van 't Hoff equation, or computing the
entropy
(approximately) using gmx covar / gmx anaeig for each of the
species.

gmx sham is just for plotting an energy landscape, e.g.
J. Mol. Biol. 354 pp. 173-183 (2005)



   What I would like now is plot the entropy and enthalpy
components

against the pull distance.  I stumbled across *gmx sham* and would


like
to
use that, however I can't find any information on how to use it
online.  I
found these posts on online forums but have found them to be
unhelpful
(I'm
sure it makes sense, it's just I am more of a chemist than a
mathematician).

*

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
hmlPKJSt/how-to-use-g-sham
<

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
hmlPKJSt/how-to-use-g-sham

*




*http://comments.gmane.org/gmane.science.biology.gromacs.use


r/64417

Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Thank you that is what I have been doing... :)

My problem is that I don't have the average COM distance for each
simulation.  Yes I specify what distance I want in the .mdp settings, but
in the earlier umbrella windows our average COM distance deviates somewhat
from the distance set in the mdp settings.  So I need a reliable way of
getting an average COM distance to match the average energy output from gmx
energy.

Best,

Billy



On 17 August 2016 at 00:28, David van der Spoel 
wrote:

> On 16/08/16 16:02, Billy Williams-Noonan wrote:
>
>> Hi David,
>>
>> Yes it's a basic question...  More about my inexperience with Gromacs than
>> anything (and maybe my chemistry background, not my math background...)
>>
>> Gmx energy gives an enthalpy against time in the .xvg output, am trying to
>> translate that to enthalpy against pull distance.
>>
>> What I had been doing was taking the mean state from each distribution in
>> the histo.xvg output, matching that up to a corresponding pull distance,
>> and assuming that the mean enthalpy from gmx energy also matched up to
>> that
>> pull distance.
>>
>> Is there a better way?
>>
> You want to average over all conformations in the simulation, same as you
> do in the PMF. So for each distance you compute the average energy with gmx
> energy and plot it.
>
>
>> Best regards,
>>
>> Billy
>> On Tuesday, 16 August 2016, David van der Spoel 
>> wrote:
>>
>> On 16/08/16 09:28, Billy Williams-Noonan wrote:
>>>
>>> Hi David,

I was wondering if you had any advice on how to plot enthalpy against
 COM pulling distance in the same manner that you have in *Figure 4*
 above?

 Maybe I don't understand the question, but I'd say you just plot the
>>> potential energy (from the energy file) with error bar for each data
>>> point
>>> and normalize to zero at infinite distance.
>>>
>>>
Best regards,

 Billy

 On 2 August 2016 at 18:15, Billy Williams-Noonan <
 billy.williams-noo...@monash.edu> wrote:

 Yes we've noticed that.  Our error estimates for enthalpy are quite high

> compared to the free energies at each umbrella window.
>
> On 2 August 2016 at 17:10, David van der Spoel 
> wrote:
>
> On 20/07/16 02:51, Billy Williams-Noonan wrote:
>
>>
>> Hi David,
>>
>>>
>>>   Thank you...!  To clarify, in Figure 4 of the paper referred to,
>>> you
>>> seem
>>> to have plotted the enthalpy of each frame against the COM pull
>>> distance
>>> and then used those values and the PMFs at each point to compute
>>> -TdS ?
>>> If
>>> so I might do something similar.
>>>
>>> Yes indeed.
>>>
>>
>> The only problem is that enthalpies converge much more slowly than
>> free
>> energies.
>>
>>
>> Billy
>>
>>>
>>> On Wednesday, 20 July 2016, David van der Spoel <
>>> sp...@xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 19/07/16 12:22, Billy Williams-Noonan wrote:
>>>
>>>
 Hi David,


>   Thank you for all your responses on here. :)  We'll have to make
> you
> an
> author if/when this gets published haha.
>
>Will try to use gmx covar / anaeig at every point but my system
> has
> 30,000 atoms so it may not be completely faesible to get an
> accurate
> value
> for the system (same problem as before).
>
> You only do this for the biomolecules separately, not the water.
>
>

Could I simply use gmx energy and get an ensemble average
 enthalpy

> for
> each point?  Then I can use the Gibbs free energy equation to solve
> for
> entropy.
>
> Yes, this is what we did in the paper :).
>
>

 Billy


> On Tuesday, 19 July 2016, David van der Spoel <
> sp...@xray.bmc.uu.se>
> wrote:
>
> On 19/07/16 09:47, Billy Williams-Noonan wrote:
>
>
> Hi All,
>>
>>
>>I have seen papers where enthalpy and entropy are plotted
>>> against
>>> the
>>> distance of a steered MD pull and am wanting to do something
>>> similar.
>>>
>>>I have run a steered MD simulation pulling a cyclic peptide
>>> out
>>> of
>>> the
>>> binding site and the PMF calculation with *gmx wham* was in
>>> reasonable
>>> agreement with experiment.  to
>>>
>>> We have published stuff like that (e.g. J. Chem. Theor. Comput. 9
>>> pp.
>>>
>>> 4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)
>>>
>> There are two main ways of doing this, rerunning the PMF at

[gmx-users] How to setup simulated tempering run?

[treinz]

Hi,


Is simulated tempering working in GROMACS 5? If so, what's the right way of 
setting it up, e.g., what combination of thermostat and integrator should be 
use? I tried using md-vv with Nose-Hoover and grompp gave me a warning about 
incompatibility. I couldn't find any reference in the manual or the user-list. 
Can someone comment on this?


Thanks,
Tim
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[gmx-users] COM-COM distance: PBC problem

[Arnost Mladek]

Dear Plumed users,

I've encountered one problem I'm unable to resolve. I use combination of 
Gromacs 5.0.4 and Plumed 2.1.3 and what I want is to calculate restrained 
distance between two center of masses (COMs) corresponding to two chains within 
a dimeric protein. If I let Plumed to calculate COM-COM distances "on-the-fly" 
(ie. during the simulation), I get correct results, let say distances in the 
interval of (4,9 ; 5.3) with the average value of 5.1 nm corresponding to the 
minimum of the restraining potential. 

If I use Plumed as a stand-alone software and calculate the distances along the 
trajectory via "plumed driver --mf_xtc trajectory.xtc --plumed pl.dat", I get 
the same correct results. Up to this point, no problem.

However if I fit (rot+trans) the trajectory frames to chain-A using GROMACS 
trjconv command (trjconv -f trajectory.xtc -s reference.tpr -o 
fitted_trajectory.xtc -fit rot+trans -center) and then run the plumed driver to 
calculate the distances from the fitted trajectory there are huge jumps of 
several nm. It is obvious that the problem is somehow associated with PBC and 
"WHOLEMOLECULES STRIDE=1 ENTITY0=protein" command within the plumed script is 
unable to resolve it. I've tried various trajectory transformations as 
suggested on GROMACS web page 
(http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions),
 like "-pbc mol -ur compact", "-pbc whole", "-pbc nojumps", etc. but nothing 
helped. As I am unable to get the COM-COM distances using GROMACS alone, I am 
not sure whether the problem relates to GROMACS or Plumed.

Thank you so much for your help.

AM
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Re: [gmx-users] Repulsive potential

[Mark Abraham]

Hi,

I've probably got no idea, but "repulsive potential" needs a lot of
clarification before the question is well formed.

Mark

On Wed, Aug 17, 2016 at 12:00 AM Mostafa Javaheri <
javaheri.grom...@gmail.com> wrote:

> Dear Justin and Mark
> Thank you for your time and consideration, that would be great too if you
> could help me with this question:
> How could I introduce repulsive potential in my simulation by using this
> feature?
> Best Regards
>
> On Wed, Aug 17, 2016 at 2:18 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > GROMACS 5.1.x also has this feature.
> >
> > Mark
> >
> > On Tue, Aug 16, 2016 at 11:37 PM Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 8/16/16 5:29 PM, Mostafa Javaheri wrote:
> > > > Dear gmx experts,
> > > >
> > > > I want to install GROMACS using
> > > > * intermolecular bonded interaction support*. Two categories of
> > patching
> > > > files uploaded in this URL https://gerrit.gromacs.org/#/c/2566/.
> > > > 1-The archive file named "6ab8ccf2".
> > > > 2- A single patch-file named "6ab8ccf2.diff".
> > > > I would be grateful if you could tell me how to patch GROMACS by
> using
> > > > these files and which GROMACS version should I use.
> > > >
> > > > Any help will be appreciated
> > > >
> > >
> > > This code was merged over a year ago, just install GROMACS-2016 and you
> > > can use
> > > the feature.
> > >
> > > -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
> > >
> > > ==
> > > --
> > > 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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> > > 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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Re: [gmx-users] Repulsive potential

[Mostafa Javaheri]

Dear Justin and Mark
Thank you for your time and consideration, that would be great too if you
could help me with this question:
How could I introduce repulsive potential in my simulation by using this
feature?
Best Regards

On Wed, Aug 17, 2016 at 2:18 AM, Mark Abraham 
wrote:

> Hi,
>
> GROMACS 5.1.x also has this feature.
>
> Mark
>
> On Tue, Aug 16, 2016 at 11:37 PM Justin Lemkul  wrote:
>
> >
> >
> > On 8/16/16 5:29 PM, Mostafa Javaheri wrote:
> > > Dear gmx experts,
> > >
> > > I want to install GROMACS using
> > > * intermolecular bonded interaction support*. Two categories of
> patching
> > > files uploaded in this URL https://gerrit.gromacs.org/#/c/2566/.
> > > 1-The archive file named "6ab8ccf2".
> > > 2- A single patch-file named "6ab8ccf2.diff".
> > > I would be grateful if you could tell me how to patch GROMACS by using
> > > these files and which GROMACS version should I use.
> > >
> > > Any help will be appreciated
> > >
> >
> > This code was merged over a year ago, just install GROMACS-2016 and you
> > can use
> > the feature.
> >
> > -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
> >
> > ==
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Repulsive potential

[Mark Abraham]

Hi,

GROMACS 5.1.x also has this feature.

Mark

On Tue, Aug 16, 2016 at 11:37 PM Justin Lemkul  wrote:

>
>
> On 8/16/16 5:29 PM, Mostafa Javaheri wrote:
> > Dear gmx experts,
> >
> > I want to install GROMACS using
> > * intermolecular bonded interaction support*. Two categories of patching
> > files uploaded in this URL https://gerrit.gromacs.org/#/c/2566/.
> > 1-The archive file named "6ab8ccf2".
> > 2- A single patch-file named "6ab8ccf2.diff".
> > I would be grateful if you could tell me how to patch GROMACS by using
> > these files and which GROMACS version should I use.
> >
> > Any help will be appreciated
> >
>
> This code was merged over a year ago, just install GROMACS-2016 and you
> can use
> the feature.
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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Re: [gmx-users] Repulsive potential

[Justin Lemkul]

On 8/16/16 5:29 PM, Mostafa Javaheri wrote:

Dear gmx experts,

I want to install GROMACS using
* intermolecular bonded interaction support*. Two categories of patching
files uploaded in this URL https://gerrit.gromacs.org/#/c/2566/.
1-The archive file named "6ab8ccf2".
2- A single patch-file named "6ab8ccf2.diff".
I would be grateful if you could tell me how to patch GROMACS by using
these files and which GROMACS version should I use.

Any help will be appreciated



This code was merged over a year ago, just install GROMACS-2016 and you can use 
the feature.


-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] Repulsive potential

[Mostafa Javaheri]

Dear gmx experts,

I want to install GROMACS using
* intermolecular bonded interaction support*. Two categories of patching
files uploaded in this URL https://gerrit.gromacs.org/#/c/2566/.
1-The archive file named "6ab8ccf2".
2- A single patch-file named "6ab8ccf2.diff".
I would be grateful if you could tell me how to patch GROMACS by using
these files and which GROMACS version should I use.

Any help will be appreciated
-- 
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Re: [gmx-users] (no subject)

[Dan Gil]

Hi,

On gromacs 4.6, the use of g_dist explicitly states "the molecule in the
input trajectory should be whole (e.g. by preprocessing with trjconv
 -pbc) or a
matching topology should be provided."
If you want to calculate the distance between the center of mass (COM) of
two groups of residues, you need to have the mass of the residues. I
imagine that you are having issues because your trajectory isn't whole. Do
you at least have the masses of the groups you are interested in? Writing
your own code to calculate the distance might be an easy solution.

On Tue, Aug 16, 2016 at 7:08 AM, Shubham Sehrawet <
shubham.cristia...@gmail.com> wrote:

> Dear users
>
> I have been trying to find distance between the centroids of two groups of
> residues. I have a trajectory file that was created on some other
> simulating platform. Therefore, I do not have the run input file (tpr) and
> I am not able to perform the analysis.
> Can you please suggest me some way to tackle the problem.
>
> Thank you
> Shubham
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Re: [gmx-users] "Fatal error: Atomtype CH2 not found" in grompp command

[Justin Lemkul]

On 8/16/16 3:04 PM, Elissa Fink wrote:

Dear Gromacs users,

I am simulating a protein-ligand complex and I am performing the grompp
command before adding ions to the system:

gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr


and I get the error:

"Source code 
file:/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,
line:1353

Fatal error:
Atomtype CH2 not found"

I checked for CH2 groups in the solv.gro file and there are 4 in tryptophan


Anything that says CH2 in a coordinate file is an atom name, not an atom type. 
The problem comes from atom types, which is a force field/topology issue.



residues. I am running the complex with the amber99sb-ildn force field. I
checked the force field .rtp file for the tryptophan name of a CH2 group.
It has CA, so I changed the 4 CH2 groups to CA in the solve.gro file. I
reran the grompp command above and got the same error. This makes me think
the problem is not the tryptophan CH2's in the solve.gro file.

Any recommendations for addressing the CH2 atom type not found?



A CH2 type is a united-atom type coming from the GROMOS force fields.  This 
means you've mixed and matched force fields, which is not appropriate.  You need 
to have a self-consistent force field representation for the 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] "Fatal error: Atomtype CH2 not found" in grompp command

[Elissa Fink]

Dear Gromacs users,

I am simulating a protein-ligand complex and I am performing the grompp
command before adding ions to the system:
>gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

and I get the error:

"Source code 
file:/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,
line:1353

Fatal error:
Atomtype CH2 not found"

I checked for CH2 groups in the solv.gro file and there are 4 in tryptophan
residues. I am running the complex with the amber99sb-ildn force field. I
checked the force field .rtp file for the tryptophan name of a CH2 group.
It has CA, so I changed the 4 CH2 groups to CA in the solve.gro file. I
reran the grompp command above and got the same error. This makes me think
the problem is not the tryptophan CH2's in the solve.gro file.

Any recommendations for addressing the CH2 atom type not found?

Thanks in advance,
Elissa Fink
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Re: [gmx-users] HID error in amber14sb.ff

[Mark Abraham]

Hi,

Please search the archives - you're not the first person to notice that
with the user-contributed port of amber14, but nobody's reported back where
the problem might be.

Mark

On Tue, Aug 16, 2016 at 7:48 PM Hongbin Wan  wrote:

> Hi all,
>
> I am trying to run MD simulations with *amber14sb.ff (downloaded from
> gromacs forcefiled web)*
>
> However, it always shows * No default Improper Dih. types *for HID when to
> use grompp. Could anyone tell me how to solve this issue?
>
> I had tried other forcefields, and they worked well.
>
> Thanks!!
> -Hongbin
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[gmx-users] HID error in amber14sb.ff

[Hongbin Wan]

Hi all,

I am trying to run MD simulations with *amber14sb.ff (downloaded from
gromacs forcefiled web)*

However, it always shows * No default Improper Dih. types *for HID when to
use grompp. Could anyone tell me how to solve this issue?

I had tried other forcefields, and they worked well.

Thanks!!
-Hongbin
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[gmx-users] Replica Exchange Solute Tempering

[shivangi nangia]

Hello All,

Is there any Replica Exchange Solute Tempering (REST) tutorial?

I specifically want to do REST2.

Please let me know.


Thanks,
sxn
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[gmx-users] number of water molecules along z

[Jagannath Mondal]

Dear Gromacs-users

  I need to compute the time profile of number of water away from a
membrane center along z direction. However trjorder -nshell -r 0.6 will
give me the number of waters along radial direction.
  there is an option in trjorder -z . but that just orders molecule along
z. but does not let one calculate water number along z at a cutoff distance.
Is there any other ways of getting it?
Jagannath
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Re: [gmx-users] CPU running doesn't match command line

[Szilárd Páll]

Most of that copy-pasted info is not what I asked for and overall not
very useful. You have still not shown any log files (or details on the
hardware). Share the *relevant* stuff, please!
--
Szilárd


On Tue, Aug 16, 2016 at 5:07 PM, Albert  wrote:
> Hello:
>
> Here is my MDP file:
>
> define  = -DREST_ON -DSTEP6_4
> integrator  = md
> dt  = 0.002
> nsteps  = 100
> nstlog  = 1000
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstcalcenergy   = 100
> nstenergy   = 1000
> nstxout-compressed  = 1
> ;
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.0
> coulombtype = pme
> rcoulomb= 1.0
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 0.9
> rvdw= 1.0
> ;
> tcoupl  = berendsen
> tc_grps = PROT   MEMB   SOL_ION
> tau_t   = 1.01.01.0
> ref_t   = 310   310   310
> ;
> pcoupl  = berendsen
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> ;
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = PROT   MEMB   SOL_ION
> ;
> refcoord_scaling= com
>
>
> I compiled Gromacs with the following settings, using Intel MPI:
>
> env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90
> CMAKE_PREFIX_PATH=/soft/gromacs/fftw-3.3.4:/soft/intel/impi/5.1.3.223 cmake
> .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
> -DCMAKE_INSTALL_PREFIX=/soft/gromacs/5.1.3_intel -DGMX_MPI=ON -DGMX_GPU=ON
> -DGMX_PREFER_STATIC_LIBS=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>
>
> I tried it again with one of the job with options:
>
> -ntomp 8 -pin on -pinoffset 8
>
>
> The two submitted jobs can still only use 8 CPU and the speed is extremely
> slow (10ns/day)when I remove option "-pin on" from one of the job, it
> fasten a lot (32ns/day) and 16 CPU were used. If I only submit one job
> with option "-pin on", I can obtain 52ns/day..
>
>
> thx a lot
>
>
> On 08/16/2016 04:59 PM, Szilárd Páll wrote:
>>
>> Hi,
>>
>> Without log and hw configs, I it's hard to tell what's happening.
>>
>> By turning off pinning the OS is free to move threads around and it
>> will try to ensure cores are utilized. However, by leaving threads
>> up-pinned you risk taking a significant performance hit. So I'd
>> recommend that you run with correct settings.
>>
>> If you start with "-ntomp 8 -pin on -pioffset 8" (and you indeed have
>> 16 cores no HT), you should be able to see in htop the first eight
>> cores empty while the last eight occupied.
>>
>> Cheers,
>> --
>> Szilárd
>
>
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Re: [gmx-users] CPU running doesn't match command line

[Albert]

Hello:

Here is my MDP file:

define  = -DREST_ON -DSTEP6_4
integrator  = md
dt  = 0.002
nsteps  = 100
nstlog  = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy   = 100
nstenergy   = 1000
nstxout-compressed  = 1
;
cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 0.9
rvdw= 1.0
;
tcoupl  = berendsen
tc_grps = PROT   MEMB   SOL_ION
tau_t   = 1.01.01.0
ref_t   = 310   310   310
;
pcoupl  = berendsen
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = PROT   MEMB   SOL_ION
;
refcoord_scaling= com


I compiled Gromacs with the following settings, using Intel MPI:

env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 
CMAKE_PREFIX_PATH=/soft/gromacs/fftw-3.3.4:/soft/intel/impi/5.1.3.223 
cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF 
-DCMAKE_INSTALL_PREFIX=/soft/gromacs/5.1.3_intel -DGMX_MPI=ON 
-DGMX_GPU=ON -DGMX_PREFER_STATIC_LIBS=ON 
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda



I tried it again with one of the job with options:

-ntomp 8 -pin on -pinoffset 8


The two submitted jobs can still only use 8 CPU and the speed is 
extremely slow (10ns/day)when I remove option "-pin on" from one of 
the job, it fasten a lot (32ns/day) and 16 CPU were used. If I only 
submit one job with option "-pin on", I can obtain 52ns/day..



thx a lot


On 08/16/2016 04:59 PM, Szilárd Páll wrote:

Hi,

Without log and hw configs, I it's hard to tell what's happening.

By turning off pinning the OS is free to move threads around and it
will try to ensure cores are utilized. However, by leaving threads
up-pinned you risk taking a significant performance hit. So I'd
recommend that you run with correct settings.

If you start with "-ntomp 8 -pin on -pioffset 8" (and you indeed have
16 cores no HT), you should be able to see in htop the first eight
cores empty while the last eight occupied.

Cheers,
--
Szilárd


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Re: [gmx-users] CPU running doesn't match command line

[Szilárd Páll]

Hi,

Without log and hw configs, I it's hard to tell what's happening.

By turning off pinning the OS is free to move threads around and it
will try to ensure cores are utilized. However, by leaving threads
up-pinned you risk taking a significant performance hit. So I'd
recommend that you run with correct settings.

If you start with "-ntomp 8 -pin on -pioffset 8" (and you indeed have
16 cores no HT), you should be able to see in htop the first eight
cores empty while the last eight occupied.

Cheers,
--
Szilárd


On Tue, Aug 16, 2016 at 4:37 PM, Albert  wrote:
> Hello:
>
> I add additional option to one of the job:
>
> -pinoffset 8
>
> to the command line. But it is still the same.However, if I remove
> option "-pin on" from one of the job, 16 CPU were occupied
>
>
>
>
> On 08/16/2016 04:18 PM, Szilárd Páll wrote:
>>
>> By starting two (piined) runs without an offset, both simulations get
>> placed on the first 8 CPUs. You should offset one of them, e.g. the
>> second, by using -pinoffset in order to have the two runs use distinct
>> set of cores.
>>
>> Cheers,
>> --
>> Szilárd
>
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] TPI and chemical potential

[João M . Damas]

I don't recall any necessary post-processing of the trajectory being
necessary, as it should deal well with PBC conditions.

I really don't know what is happening, but it seems like the fixes are
going in the right direction.

Try to plot the  along time, to see if it's converging or not.
Depending on the trend, you may want to extend the simulation time. Other
reasons for incorrect excess chemical potential may be that the TIP3p model
may not reproduce well that quantity.

And yeah, it's kJ/mol.

João

On Tue, Aug 16, 2016 at 2:12 PM, Gmx QA  wrote:

> Thanks Joao
>
> The water box is equilibrated at 298K (I checked density and temperature
>  with gmx energy, and they show no drift from reasonable averages).
>
> However, I am a bit confused as I just tried the approach on the same
> trajectory, but extended to 2.5 ns and after one pass through trjconv with
> -pbc mol -ur compact options.
>
> This seems to work in the sense that I no longer get any infs, but the
> value of , while having the right magnitude, is still off by about a
> factor of 2.
> After 2.5 ns I get  = -45 (I assume the unit is kJ/mol), whereas if i
> read correctly the chemical potential should be -23.5 or so. Can it be that
> I now need to increase the run time of my water simulation even more?
>
> Thanks
> /PK
>
>
>
> 2016-08-16 13:47 GMT+02:00 João M. Damas :
>
> > Well, 5 insertions per frame, doesn't look bad. 1 ns should not be an
> > issue.
> >
> > Well, actually that value normally starts at inf and should go to the
> > equilibrium  as you increase sampling. But to be inf after 5
> > inserts, it does sound weird.
> >
> > How did you build your box of water? Is it equilibrated at that
> temperature
> > (298 K)?
> > Please make make that the water molecule to be inserted has the correct
> > geometrical coordinates and that it is centered at 0,0,0.
> >
> > João
> >
> > On Tue, Aug 16, 2016 at 12:45 PM, Gmx QA  wrote:
> >
> > > Hi Joao
> > >
> > > Thank you for your reply. My mdp-file is pasted below:
> > >
> > > integrator  = tpi
> > > emtol = 1000.0
> > > emstep  = 0.01
> > > nsteps= 5
> > >
> > > nstlist = 1
> > > cutoff-scheme   = group
> > > ns_type = grid
> > > coulombtype = pme
> > > rcoulomb= 1.0
> > > rvdw= 1.0
> > > pbc = xyz
> > > nstxtcout = 5000
> > >
> > > ; Temperature coupling is on
> > > tcoupl = V-rescale
> > > tc-grps  = system
> > > tau_t  = 0.1
> > > ref_t= 298
> > >
> > > ; Pressure coupling is on
> > > pcoupl  = no
> > > pcoupltype  = isotropic
> > > tau_p   = 2.0
> > > ref_p   = 1.0
> > > compressibility = 4.5e-5
> > >
> > > ld_seed = -1
> > >
> > > I am using the amber99sb forcefield for tip3p, so I believe the 1.0 nm
> > > cutoffs to be correct?
> > >
> > > I have tried a couple different values for the number of insertions,
> and
> > > for some frames different values sometimes give non-inf results, but
> for
> > > the most part it does not seem to make a difference.
> > >
> > > 1 ns is short, I agree, but since the value of  (which I take to be
> > the
> > > excess chemical potential I am after) immediately goes to inf when the
> > > first mu=inf appears, extending does not make sense to me? Is the
> > chemical
> > > potential reported elsewhere as well?
> > >
> > > Thanks
> > > /PK
> > >
> > > 2016-08-16 12:35 GMT+02:00 João M. Damas :
> > >
> > > > Yes, all water atoms can't be with coordinates 0,0,0. I don't know
> how
> > > did
> > > > that even work... Weird.
> > > >
> > > > 1 ns is very short time scale. Also, how many insertions are you
> trying
> > > per
> > > > frame? That could also help improve the sampling.
> > > >
> > > > The inf values are normal as it just means that the water is too
> > > structured
> > > > and it's hard to insert a new water from the sampling point of view.
> > > >
> > > > Can you post the .mdp you used for the tpi?
> > > >
> > > > João
> > > >
> > > > On Tue, Aug 16, 2016 at 9:52 AM, Gmx QA 
> > wrote:
> > > >
> > > > > Please - anyone?
> > > > >
> > > > > I gathered from the mail-list that maybe the entire molecule (water
> > in
> > > > this
> > > > > case) should be centered on origo (rather than having all atoms at
> > > > (0,0,0),
> > > > > but this gives me only a lot of inf for the chemical potential.
> > > > >
> > > > > How can I calculate the excess chemical potential of water using
> TPI
> > in
> > > > > gromacs?
> > > > >
> > > > >
> > > > >
> > > > > 2016-08-15 13:31 GMT+02:00 Gmx QA :
> > > > >
> > > > > > Dear list
> > > > > >
> > > > > > I am trying to teach myself how the test particle method for
> excess
> > > > > > chemical potential calculations work. To this end, I 

Re: [gmx-users] CPU running doesn't match command line

[Albert]

Hello:

I add additional option to one of the job:

-pinoffset 8

to the command line. But it is still the same.However, if I 
remove option "-pin on" from one of the job, 16 CPU were occupied





On 08/16/2016 04:18 PM, Szilárd Páll wrote:

By starting two (piined) runs without an offset, both simulations get
placed on the first 8 CPUs. You should offset one of them, e.g. the
second, by using -pinoffset in order to have the two runs use distinct
set of cores.

Cheers,
--
Szilárd


--
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Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[David van der Spoel]

On 16/08/16 16:02, Billy Williams-Noonan wrote:

Hi David,

Yes it's a basic question...  More about my inexperience with Gromacs than
anything (and maybe my chemistry background, not my math background...)

Gmx energy gives an enthalpy against time in the .xvg output, am trying to
translate that to enthalpy against pull distance.

What I had been doing was taking the mean state from each distribution in
the histo.xvg output, matching that up to a corresponding pull distance,
and assuming that the mean enthalpy from gmx energy also matched up to that
pull distance.

Is there a better way?
You want to average over all conformations in the simulation, same as 
you do in the PMF. So for each distance you compute the average energy 
with gmx energy and plot it.


Best regards,

Billy
On Tuesday, 16 August 2016, David van der Spoel 
wrote:


On 16/08/16 09:28, Billy Williams-Noonan wrote:


Hi David,

   I was wondering if you had any advice on how to plot enthalpy against
COM pulling distance in the same manner that you have in *Figure 4* above?


Maybe I don't understand the question, but I'd say you just plot the
potential energy (from the energy file) with error bar for each data point
and normalize to zero at infinite distance.



   Best regards,

Billy

On 2 August 2016 at 18:15, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

Yes we've noticed that.  Our error estimates for enthalpy are quite high

compared to the free energies at each umbrella window.

On 2 August 2016 at 17:10, David van der Spoel 
wrote:

On 20/07/16 02:51, Billy Williams-Noonan wrote:


Hi David,


  Thank you...!  To clarify, in Figure 4 of the paper referred to, you
seem
to have plotted the enthalpy of each frame against the COM pull
distance
and then used those values and the PMFs at each point to compute -TdS ?
If
so I might do something similar.

Yes indeed.


The only problem is that enthalpies converge much more slowly than free
energies.


Billy


On Wednesday, 20 July 2016, David van der Spoel 
wrote:

On 19/07/16 12:22, Billy Williams-Noonan wrote:



Hi David,



  Thank you for all your responses on here. :)  We'll have to make
you
an
author if/when this gets published haha.

   Will try to use gmx covar / anaeig at every point but my system
has
30,000 atoms so it may not be completely faesible to get an accurate
value
for the system (same problem as before).

You only do this for the biomolecules separately, not the water.




   Could I simply use gmx energy and get an ensemble average enthalpy

for
each point?  Then I can use the Gibbs free energy equation to solve
for
entropy.

Yes, this is what we did in the paper :).




Billy



On Tuesday, 19 July 2016, David van der Spoel 
wrote:

On 19/07/16 09:47, Billy Williams-Noonan wrote:



Hi All,



   I have seen papers where enthalpy and entropy are plotted
against
the
distance of a steered MD pull and am wanting to do something
similar.

   I have run a steered MD simulation pulling a cyclic peptide out
of
the
binding site and the PMF calculation with *gmx wham* was in
reasonable
agreement with experiment.  to

We have published stuff like that (e.g. J. Chem. Theor. Comput. 9
pp.

4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)

There are two main ways of doing this, rerunning the PMF at
different
temperatures and using the Van 't Hoff equation, or computing the
entropy
(approximately) using gmx covar / gmx anaeig for each of the
species.

gmx sham is just for plotting an energy landscape, e.g.
J. Mol. Biol. 354 pp. 173-183 (2005)



   What I would like now is plot the entropy and enthalpy components

against the pull distance.  I stumbled across *gmx sham* and would

like
to
use that, however I can't find any information on how to use it
online.  I
found these posts on online forums but have found them to be
unhelpful
(I'm
sure it makes sense, it's just I am more of a chemist than a
mathematician).

*

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
hmlPKJSt/how-to-use-g-sham
<

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
hmlPKJSt/how-to-use-g-sham

*




*http://comments.gmane.org/gmane.science.biology.gromacs.use

r/64417
*

   Could someone please let me know the exact commands I need to
use
with
*gmx
sham i*n order to plot entropy and enthalpy against the pull
distance?

   Kind regards,

Billy



--


David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Gromacs Users 

Re: [gmx-users] CPU running doesn't match command line

[Szilárd Páll]

By starting two (piined) runs without an offset, both simulations get
placed on the first 8 CPUs. You should offset one of them, e.g. the
second, by using -pinoffset in order to have the two runs use distinct
set of cores.

Cheers,
--
Szilárd


On Tue, Aug 16, 2016 at 3:55 PM, Albert  wrote:
> Hello:
>
> I submitted two Gromacs GPU MD simulation to the same GPU machine with the
> identical command line:
>
> gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 0 -pin
> on >& 7.info
> gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 1 -pin
> on >& 7.info
>
> In principle, there should be 16 CPU in all  were occupied by these two
> jobs. However, I found that (by command htop) there are only actually 8 CPU
> using, although it created 16 thread job. I am just wondering what's
> happening? If I only submit one job, 8 CPU are occupied.
>
> Thank you very much.
>
> Albert
> --
> Gromacs Users mailing list
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Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Hi David,

Yes it's a basic question...  More about my inexperience with Gromacs than
anything (and maybe my chemistry background, not my math background...)

Gmx energy gives an enthalpy against time in the .xvg output, am trying to
translate that to enthalpy against pull distance.

What I had been doing was taking the mean state from each distribution in
the histo.xvg output, matching that up to a corresponding pull distance,
and assuming that the mean enthalpy from gmx energy also matched up to that
pull distance.

Is there a better way?

Best regards,

Billy
On Tuesday, 16 August 2016, David van der Spoel 
wrote:

> On 16/08/16 09:28, Billy Williams-Noonan wrote:
>
>> Hi David,
>>
>>I was wondering if you had any advice on how to plot enthalpy against
>> COM pulling distance in the same manner that you have in *Figure 4* above?
>>
> Maybe I don't understand the question, but I'd say you just plot the
> potential energy (from the energy file) with error bar for each data point
> and normalize to zero at infinite distance.
>
>>
>>Best regards,
>>
>> Billy
>>
>> On 2 August 2016 at 18:15, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Yes we've noticed that.  Our error estimates for enthalpy are quite high
>>> compared to the free energies at each umbrella window.
>>>
>>> On 2 August 2016 at 17:10, David van der Spoel 
>>> wrote:
>>>
>>> On 20/07/16 02:51, Billy Williams-Noonan wrote:

 Hi David,
>
>   Thank you...!  To clarify, in Figure 4 of the paper referred to, you
> seem
> to have plotted the enthalpy of each frame against the COM pull
> distance
> and then used those values and the PMFs at each point to compute -TdS ?
> If
> so I might do something similar.
>
> Yes indeed.

 The only problem is that enthalpies converge much more slowly than free
 energies.


 Billy
>
> On Wednesday, 20 July 2016, David van der Spoel 
> wrote:
>
> On 19/07/16 12:22, Billy Williams-Noonan wrote:
>
>>
>> Hi David,
>>
>>>
>>>   Thank you for all your responses on here. :)  We'll have to make
>>> you
>>> an
>>> author if/when this gets published haha.
>>>
>>>Will try to use gmx covar / anaeig at every point but my system
>>> has
>>> 30,000 atoms so it may not be completely faesible to get an accurate
>>> value
>>> for the system (same problem as before).
>>>
>>> You only do this for the biomolecules separately, not the water.
>>>
>>
>>
>>Could I simply use gmx energy and get an ensemble average enthalpy
>>> for
>>> each point?  Then I can use the Gibbs free energy equation to solve
>>> for
>>> entropy.
>>>
>>> Yes, this is what we did in the paper :).
>>>
>>
>>
>> Billy
>>
>>>
>>> On Tuesday, 19 July 2016, David van der Spoel 
>>> wrote:
>>>
>>> On 19/07/16 09:47, Billy Williams-Noonan wrote:
>>>
>>>
 Hi All,


>I have seen papers where enthalpy and entropy are plotted
> against
> the
> distance of a steered MD pull and am wanting to do something
> similar.
>
>I have run a steered MD simulation pulling a cyclic peptide out
> of
> the
> binding site and the PMF calculation with *gmx wham* was in
> reasonable
> agreement with experiment.  to
>
> We have published stuff like that (e.g. J. Chem. Theor. Comput. 9
> pp.
>
> 4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)
 There are two main ways of doing this, rerunning the PMF at
 different
 temperatures and using the Van 't Hoff equation, or computing the
 entropy
 (approximately) using gmx covar / gmx anaeig for each of the
 species.

 gmx sham is just for plotting an energy landscape, e.g.
 J. Mol. Biol. 354 pp. 173-183 (2005)



What I would like now is plot the entropy and enthalpy components

 against the pull distance.  I stumbled across *gmx sham* and would
> like
> to
> use that, however I can't find any information on how to use it
> online.  I
> found these posts on online forums but have found them to be
> unhelpful
> (I'm
> sure it makes sense, it's just I am more of a chemist than a
> mathematician).
>
> *
>
> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
> hmlPKJSt/how-to-use-g-sham
> <
>
> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
> hmlPKJSt/how-to-use-g-sham
>
> *
>
>>
>>

[gmx-users] CPU running doesn't match command line

[Albert]

Hello:

I submitted two Gromacs GPU MD simulation to the same GPU machine with 
the identical command line:


gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 0 
-pin on >& 7.info
gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 1 
-pin on >& 7.info


In principle, there should be 16 CPU in all  were occupied by these two 
jobs. However, I found that (by command htop) there are only actually 8 
CPU using, although it created 16 thread job. I am just wondering 
what's happening? If I only submit one job, 8 CPU are occupied.


Thank you very much.

Albert
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Re: [gmx-users] Gromacs does not fully utilize CPU

[Mark Abraham]

Hi,

Such node sharing is definitely going to hurt your throughput - mdrun is
designed to saturate the CPU cores you run it on. Just starting both
processes naively will give terrible performance. You have to keep both
processes on separate cores (e.g. with Linux taskset or similar tools to
set the *affinity* of the threads to cores). mdrun can also be managed
along the lines of
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node
but
your other process will need some other kind of management, so you might as
well use the same for mdrun (which by default it will respect).

Mark

On Tue, Aug 16, 2016 at 2:44 PM Irem Altan  wrote:

> Hi,
>
> I have a system with an nVidia Tesla K20 and 12 cores with
> hyper-threading. It normally runs with %2400 CPU. However, when there is
> another process working, taking up 50% CPU, Gromacs ends up using 1500% CPU
> instead. This results in only 67% of the total CPU being utilized. Is this
> expected behavior? If so, what is the best way to optimize the system?
>
> Best,
> Irem
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] TPI and chemical potential

[Gmx QA]

Thanks Joao

The water box is equilibrated at 298K (I checked density and temperature
 with gmx energy, and they show no drift from reasonable averages).

However, I am a bit confused as I just tried the approach on the same
trajectory, but extended to 2.5 ns and after one pass through trjconv with
-pbc mol -ur compact options.

This seems to work in the sense that I no longer get any infs, but the
value of , while having the right magnitude, is still off by about a
factor of 2.
After 2.5 ns I get  = -45 (I assume the unit is kJ/mol), whereas if i
read correctly the chemical potential should be -23.5 or so. Can it be that
I now need to increase the run time of my water simulation even more?

Thanks
/PK



2016-08-16 13:47 GMT+02:00 João M. Damas :

> Well, 5 insertions per frame, doesn't look bad. 1 ns should not be an
> issue.
>
> Well, actually that value normally starts at inf and should go to the
> equilibrium  as you increase sampling. But to be inf after 5
> inserts, it does sound weird.
>
> How did you build your box of water? Is it equilibrated at that temperature
> (298 K)?
> Please make make that the water molecule to be inserted has the correct
> geometrical coordinates and that it is centered at 0,0,0.
>
> João
>
> On Tue, Aug 16, 2016 at 12:45 PM, Gmx QA  wrote:
>
> > Hi Joao
> >
> > Thank you for your reply. My mdp-file is pasted below:
> >
> > integrator  = tpi
> > emtol = 1000.0
> > emstep  = 0.01
> > nsteps= 5
> >
> > nstlist = 1
> > cutoff-scheme   = group
> > ns_type = grid
> > coulombtype = pme
> > rcoulomb= 1.0
> > rvdw= 1.0
> > pbc = xyz
> > nstxtcout = 5000
> >
> > ; Temperature coupling is on
> > tcoupl = V-rescale
> > tc-grps  = system
> > tau_t  = 0.1
> > ref_t= 298
> >
> > ; Pressure coupling is on
> > pcoupl  = no
> > pcoupltype  = isotropic
> > tau_p   = 2.0
> > ref_p   = 1.0
> > compressibility = 4.5e-5
> >
> > ld_seed = -1
> >
> > I am using the amber99sb forcefield for tip3p, so I believe the 1.0 nm
> > cutoffs to be correct?
> >
> > I have tried a couple different values for the number of insertions, and
> > for some frames different values sometimes give non-inf results, but for
> > the most part it does not seem to make a difference.
> >
> > 1 ns is short, I agree, but since the value of  (which I take to be
> the
> > excess chemical potential I am after) immediately goes to inf when the
> > first mu=inf appears, extending does not make sense to me? Is the
> chemical
> > potential reported elsewhere as well?
> >
> > Thanks
> > /PK
> >
> > 2016-08-16 12:35 GMT+02:00 João M. Damas :
> >
> > > Yes, all water atoms can't be with coordinates 0,0,0. I don't know how
> > did
> > > that even work... Weird.
> > >
> > > 1 ns is very short time scale. Also, how many insertions are you trying
> > per
> > > frame? That could also help improve the sampling.
> > >
> > > The inf values are normal as it just means that the water is too
> > structured
> > > and it's hard to insert a new water from the sampling point of view.
> > >
> > > Can you post the .mdp you used for the tpi?
> > >
> > > João
> > >
> > > On Tue, Aug 16, 2016 at 9:52 AM, Gmx QA 
> wrote:
> > >
> > > > Please - anyone?
> > > >
> > > > I gathered from the mail-list that maybe the entire molecule (water
> in
> > > this
> > > > case) should be centered on origo (rather than having all atoms at
> > > (0,0,0),
> > > > but this gives me only a lot of inf for the chemical potential.
> > > >
> > > > How can I calculate the excess chemical potential of water using TPI
> in
> > > > gromacs?
> > > >
> > > >
> > > >
> > > > 2016-08-15 13:31 GMT+02:00 Gmx QA :
> > > >
> > > > > Dear list
> > > > >
> > > > > I am trying to teach myself how the test particle method for excess
> > > > > chemical potential calculations work. To this end, I created a
> small
> > > > system
> > > > > of about 900 water molecules (TIP3p), and simulated for 1 ns.
> > > > >
> > > > > I then set up files for inserting an extra water molecule to
> > calculate
> > > > mu,
> > > > > the chemical potential.
> > > > >
> > > > > The end of my tpi_start.gro looks like this:
> > > > > 
> > > > >   884SOL OW 2650   2.466   0.788   2.747 -0.5599 -0.0387
> 0.0570
> > > > >   884SOLHW1 2651   2.529   0.835   2.802  0.0024 -0.9901
> 0.2261
> > > > >   884SOLHW2 2652   2.506   0.703   2.732 -1.4472 -0.3598
> -0.5022
> > > > >   885SOL OW 2653   0.000   0.000   0.000  0.  0.
> 0.
> > > > >   885SOLHW1 2654   0.000   0.000   0.000  0.  0.
> 0.
> > > > >   885SOLHW2 2655   0.000   0.000   0.000  0.  0.
> 0.
> > > > >3.01188   3.01188   3.01188
> > > > >

Re: [gmx-users] TPI and chemical potential

[João M . Damas]

Well, 5 insertions per frame, doesn't look bad. 1 ns should not be an
issue.

Well, actually that value normally starts at inf and should go to the
equilibrium  as you increase sampling. But to be inf after 5
inserts, it does sound weird.

How did you build your box of water? Is it equilibrated at that temperature
(298 K)?
Please make make that the water molecule to be inserted has the correct
geometrical coordinates and that it is centered at 0,0,0.

João

On Tue, Aug 16, 2016 at 12:45 PM, Gmx QA  wrote:

> Hi Joao
>
> Thank you for your reply. My mdp-file is pasted below:
>
> integrator  = tpi
> emtol = 1000.0
> emstep  = 0.01
> nsteps= 5
>
> nstlist = 1
> cutoff-scheme   = group
> ns_type = grid
> coulombtype = pme
> rcoulomb= 1.0
> rvdw= 1.0
> pbc = xyz
> nstxtcout = 5000
>
> ; Temperature coupling is on
> tcoupl = V-rescale
> tc-grps  = system
> tau_t  = 0.1
> ref_t= 298
>
> ; Pressure coupling is on
> pcoupl  = no
> pcoupltype  = isotropic
> tau_p   = 2.0
> ref_p   = 1.0
> compressibility = 4.5e-5
>
> ld_seed = -1
>
> I am using the amber99sb forcefield for tip3p, so I believe the 1.0 nm
> cutoffs to be correct?
>
> I have tried a couple different values for the number of insertions, and
> for some frames different values sometimes give non-inf results, but for
> the most part it does not seem to make a difference.
>
> 1 ns is short, I agree, but since the value of  (which I take to be the
> excess chemical potential I am after) immediately goes to inf when the
> first mu=inf appears, extending does not make sense to me? Is the chemical
> potential reported elsewhere as well?
>
> Thanks
> /PK
>
> 2016-08-16 12:35 GMT+02:00 João M. Damas :
>
> > Yes, all water atoms can't be with coordinates 0,0,0. I don't know how
> did
> > that even work... Weird.
> >
> > 1 ns is very short time scale. Also, how many insertions are you trying
> per
> > frame? That could also help improve the sampling.
> >
> > The inf values are normal as it just means that the water is too
> structured
> > and it's hard to insert a new water from the sampling point of view.
> >
> > Can you post the .mdp you used for the tpi?
> >
> > João
> >
> > On Tue, Aug 16, 2016 at 9:52 AM, Gmx QA  wrote:
> >
> > > Please - anyone?
> > >
> > > I gathered from the mail-list that maybe the entire molecule (water in
> > this
> > > case) should be centered on origo (rather than having all atoms at
> > (0,0,0),
> > > but this gives me only a lot of inf for the chemical potential.
> > >
> > > How can I calculate the excess chemical potential of water using TPI in
> > > gromacs?
> > >
> > >
> > >
> > > 2016-08-15 13:31 GMT+02:00 Gmx QA :
> > >
> > > > Dear list
> > > >
> > > > I am trying to teach myself how the test particle method for excess
> > > > chemical potential calculations work. To this end, I created a small
> > > system
> > > > of about 900 water molecules (TIP3p), and simulated for 1 ns.
> > > >
> > > > I then set up files for inserting an extra water molecule to
> calculate
> > > mu,
> > > > the chemical potential.
> > > >
> > > > The end of my tpi_start.gro looks like this:
> > > > 
> > > >   884SOL OW 2650   2.466   0.788   2.747 -0.5599 -0.0387  0.0570
> > > >   884SOLHW1 2651   2.529   0.835   2.802  0.0024 -0.9901  0.2261
> > > >   884SOLHW2 2652   2.506   0.703   2.732 -1.4472 -0.3598 -0.5022
> > > >   885SOL OW 2653   0.000   0.000   0.000  0.  0.  0.
> > > >   885SOLHW1 2654   0.000   0.000   0.000  0.  0.  0.
> > > >   885SOLHW2 2655   0.000   0.000   0.000  0.  0.  0.
> > > >3.01188   3.01188   3.01188
> > > >
> > > > So I think this last water molecule is the one to be inserted. The
> > > > topology was also updated accordingly.
> > > >
> > > > I then made a rerun like this:
> > > >
> > > > $ gmx mdrun -v -deffnm tpi -rerun md.xtc
> > > >
> > > > And the output is a series of lines like this:
> > > >
> > > > Reading frame 180 time  900.000   mu  8.924e+00   7.240e+00
> > > > mu  7.671e+00   7.242e+00
> > > > mu  6.987e+00   7.241e+00
> > > > mu  7.010e+00   7.239e+00
> > > > mu  7.691e+00   7.241e+00
> > > > mu  7.439e+00   7.242e+00
> > > > mu  6.757e+00   7.240e+00
> > > > mu  8.114e+00   7.243e+00
> > > > mu  7.173e+00   7.243e+00
> > > > mu  8.768e+00   7.249e+00
> > > > Reading frame 190 time  950.000   mu  7.799e+00   7.252e+00
> > > > mu  9.284e+00   7.259e+00
> > > > mu  8.103e+00   7.262e+00
> > > > mu  7.835e+00   7.265e+00
> > > > mu  7.321e+00   7.265e+00
> > > > mu  7.576e+00   7.267e+00
> > > > mu  9.348e+00   7.274e+00
> > > > mu  7.021e+00   7.272e+00
> > > > mu  7.162e+00   7.272e+00
> > > > mu  

[gmx-users] (no subject)

[Shubham Sehrawet]

Dear users

I have been trying to find distance between the centroids of two groups of
residues. I have a trajectory file that was created on some other
simulating platform. Therefore, I do not have the run input file (tpr) and
I am not able to perform the analysis.
Can you please suggest me some way to tackle the problem.

Thank you
Shubham
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Re: [gmx-users] TPI and chemical potential

[Gmx QA]

Hi Joao

Thank you for your reply. My mdp-file is pasted below:

integrator  = tpi
emtol = 1000.0
emstep  = 0.01
nsteps= 5

nstlist = 1
cutoff-scheme   = group
ns_type = grid
coulombtype = pme
rcoulomb= 1.0
rvdw= 1.0
pbc = xyz
nstxtcout = 5000

; Temperature coupling is on
tcoupl = V-rescale
tc-grps  = system
tau_t  = 0.1
ref_t= 298

; Pressure coupling is on
pcoupl  = no
pcoupltype  = isotropic
tau_p   = 2.0
ref_p   = 1.0
compressibility = 4.5e-5

ld_seed = -1

I am using the amber99sb forcefield for tip3p, so I believe the 1.0 nm
cutoffs to be correct?

I have tried a couple different values for the number of insertions, and
for some frames different values sometimes give non-inf results, but for
the most part it does not seem to make a difference.

1 ns is short, I agree, but since the value of  (which I take to be the
excess chemical potential I am after) immediately goes to inf when the
first mu=inf appears, extending does not make sense to me? Is the chemical
potential reported elsewhere as well?

Thanks
/PK

2016-08-16 12:35 GMT+02:00 João M. Damas :

> Yes, all water atoms can't be with coordinates 0,0,0. I don't know how did
> that even work... Weird.
>
> 1 ns is very short time scale. Also, how many insertions are you trying per
> frame? That could also help improve the sampling.
>
> The inf values are normal as it just means that the water is too structured
> and it's hard to insert a new water from the sampling point of view.
>
> Can you post the .mdp you used for the tpi?
>
> João
>
> On Tue, Aug 16, 2016 at 9:52 AM, Gmx QA  wrote:
>
> > Please - anyone?
> >
> > I gathered from the mail-list that maybe the entire molecule (water in
> this
> > case) should be centered on origo (rather than having all atoms at
> (0,0,0),
> > but this gives me only a lot of inf for the chemical potential.
> >
> > How can I calculate the excess chemical potential of water using TPI in
> > gromacs?
> >
> >
> >
> > 2016-08-15 13:31 GMT+02:00 Gmx QA :
> >
> > > Dear list
> > >
> > > I am trying to teach myself how the test particle method for excess
> > > chemical potential calculations work. To this end, I created a small
> > system
> > > of about 900 water molecules (TIP3p), and simulated for 1 ns.
> > >
> > > I then set up files for inserting an extra water molecule to calculate
> > mu,
> > > the chemical potential.
> > >
> > > The end of my tpi_start.gro looks like this:
> > > 
> > >   884SOL OW 2650   2.466   0.788   2.747 -0.5599 -0.0387  0.0570
> > >   884SOLHW1 2651   2.529   0.835   2.802  0.0024 -0.9901  0.2261
> > >   884SOLHW2 2652   2.506   0.703   2.732 -1.4472 -0.3598 -0.5022
> > >   885SOL OW 2653   0.000   0.000   0.000  0.  0.  0.
> > >   885SOLHW1 2654   0.000   0.000   0.000  0.  0.  0.
> > >   885SOLHW2 2655   0.000   0.000   0.000  0.  0.  0.
> > >3.01188   3.01188   3.01188
> > >
> > > So I think this last water molecule is the one to be inserted. The
> > > topology was also updated accordingly.
> > >
> > > I then made a rerun like this:
> > >
> > > $ gmx mdrun -v -deffnm tpi -rerun md.xtc
> > >
> > > And the output is a series of lines like this:
> > >
> > > Reading frame 180 time  900.000   mu  8.924e+00   7.240e+00
> > > mu  7.671e+00   7.242e+00
> > > mu  6.987e+00   7.241e+00
> > > mu  7.010e+00   7.239e+00
> > > mu  7.691e+00   7.241e+00
> > > mu  7.439e+00   7.242e+00
> > > mu  6.757e+00   7.240e+00
> > > mu  8.114e+00   7.243e+00
> > > mu  7.173e+00   7.243e+00
> > > mu  8.768e+00   7.249e+00
> > > Reading frame 190 time  950.000   mu  7.799e+00   7.252e+00
> > > mu  9.284e+00   7.259e+00
> > > mu  8.103e+00   7.262e+00
> > > mu  7.835e+00   7.265e+00
> > > mu  7.321e+00   7.265e+00
> > > mu  7.576e+00   7.267e+00
> > > mu  9.348e+00   7.274e+00
> > > mu  7.021e+00   7.272e+00
> > > mu  7.162e+00   7.272e+00
> > > mu  7.695e+00   7.274e+00
> > > Reading frame 200 time 1000.000   mu  7.104e+00   7.273e+00
> > >
> > > Now, is  here the average computed chemical potential? What is the
> > TPI
> > > energy distribution being reported in the tpi.xvg-file?
> > >
> > > I tried to google for the chemical potential of water and according to
> > > e.g. [1] (page 13) it should be around -23.5 kJ/mol. I would really
> > > appreciate if someone could comment on this, as I need to understand it
> > > before moving on to more relevant (for me) systems….
> > >
> > > Thanks
> > > /PK
> > >
> > >
> > >
> > >
> > >
> > > [1] Chemical potential of liquids and mixtures via Adaptive Resolution
> > ...
> > >  > cd=21=0ahUKEwj-7-2gqMPOAhVFWiwKHdp4DYY4FBAWCBww
> > 

Re: [gmx-users] TPI and chemical potential

[João M . Damas]

Yes, all water atoms can't be with coordinates 0,0,0. I don't know how did
that even work... Weird.

1 ns is very short time scale. Also, how many insertions are you trying per
frame? That could also help improve the sampling.

The inf values are normal as it just means that the water is too structured
and it's hard to insert a new water from the sampling point of view.

Can you post the .mdp you used for the tpi?

João

On Tue, Aug 16, 2016 at 9:52 AM, Gmx QA  wrote:

> Please - anyone?
>
> I gathered from the mail-list that maybe the entire molecule (water in this
> case) should be centered on origo (rather than having all atoms at (0,0,0),
> but this gives me only a lot of inf for the chemical potential.
>
> How can I calculate the excess chemical potential of water using TPI in
> gromacs?
>
>
>
> 2016-08-15 13:31 GMT+02:00 Gmx QA :
>
> > Dear list
> >
> > I am trying to teach myself how the test particle method for excess
> > chemical potential calculations work. To this end, I created a small
> system
> > of about 900 water molecules (TIP3p), and simulated for 1 ns.
> >
> > I then set up files for inserting an extra water molecule to calculate
> mu,
> > the chemical potential.
> >
> > The end of my tpi_start.gro looks like this:
> > 
> >   884SOL OW 2650   2.466   0.788   2.747 -0.5599 -0.0387  0.0570
> >   884SOLHW1 2651   2.529   0.835   2.802  0.0024 -0.9901  0.2261
> >   884SOLHW2 2652   2.506   0.703   2.732 -1.4472 -0.3598 -0.5022
> >   885SOL OW 2653   0.000   0.000   0.000  0.  0.  0.
> >   885SOLHW1 2654   0.000   0.000   0.000  0.  0.  0.
> >   885SOLHW2 2655   0.000   0.000   0.000  0.  0.  0.
> >3.01188   3.01188   3.01188
> >
> > So I think this last water molecule is the one to be inserted. The
> > topology was also updated accordingly.
> >
> > I then made a rerun like this:
> >
> > $ gmx mdrun -v -deffnm tpi -rerun md.xtc
> >
> > And the output is a series of lines like this:
> >
> > Reading frame 180 time  900.000   mu  8.924e+00   7.240e+00
> > mu  7.671e+00   7.242e+00
> > mu  6.987e+00   7.241e+00
> > mu  7.010e+00   7.239e+00
> > mu  7.691e+00   7.241e+00
> > mu  7.439e+00   7.242e+00
> > mu  6.757e+00   7.240e+00
> > mu  8.114e+00   7.243e+00
> > mu  7.173e+00   7.243e+00
> > mu  8.768e+00   7.249e+00
> > Reading frame 190 time  950.000   mu  7.799e+00   7.252e+00
> > mu  9.284e+00   7.259e+00
> > mu  8.103e+00   7.262e+00
> > mu  7.835e+00   7.265e+00
> > mu  7.321e+00   7.265e+00
> > mu  7.576e+00   7.267e+00
> > mu  9.348e+00   7.274e+00
> > mu  7.021e+00   7.272e+00
> > mu  7.162e+00   7.272e+00
> > mu  7.695e+00   7.274e+00
> > Reading frame 200 time 1000.000   mu  7.104e+00   7.273e+00
> >
> > Now, is  here the average computed chemical potential? What is the
> TPI
> > energy distribution being reported in the tpi.xvg-file?
> >
> > I tried to google for the chemical potential of water and according to
> > e.g. [1] (page 13) it should be around -23.5 kJ/mol. I would really
> > appreciate if someone could comment on this, as I need to understand it
> > before moving on to more relevant (for me) systems….
> >
> > Thanks
> > /PK
> >
> >
> >
> >
> >
> > [1] Chemical potential of liquids and mixtures via Adaptive Resolution
> ...
> >  cd=21=0ahUKEwj-7-2gqMPOAhVFWiwKHdp4DYY4FBAWCBww
> AA=https%3A%2F%2Fopus4.kobv.de%2Fopus4-zib%2Ffiles%
> 2F5097%2FZIB-Report_14-25.pdf=AFQjCNECRk9dif8TGxKJeeztHV6T_
> FmVuw=-vsjUB9HRdlcnt4vyKWcbw>
> >
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [gmx-users] Loosing partly the available CPU time

[Alexander Alexander]

Hi Szila

I tried more more OpenMP threads, (-ntomp 4), however, the performance
dropped down drastically so that an NVT simulation which just took 3 hours
to be finished in "-ntomp 1", now takes more thank 16 hours!

Cheers,
Alex

On Mon, Aug 15, 2016 at 6:34 PM, Szilárd Páll 
wrote:

> Hi,
>
> Although I don't know what exactly is the system you are simulating,
> one thing is clear: you're pushing the parallelization limit with
> - 200 atoms/core
> - likely "concentrated" free energy interactions.
> The former that alone will make the run very sensitive to load
> imbalance and the latter makes imbalance even worse as the very
> expensive free energy interactions likely all fall in a few domains
> (unless your 8 perturbed atoms are scattered).
>
> There is not much you can do except the what I previously suggested
> (trying more OpenMP threads e.g. 2-4 or simply use less cores). If you
> have the possibility, using some hardware with fewer and faster cores
> (and perhaps a GPU) will also be much more suitable than this 128-core
> AMD node.
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Aug 15, 2016 at 4:01 PM, Alexander Alexander
>  wrote:
> > Hi Szilárd,
> >
> > Thanks for your response, please find below a link containing required
> > files.log files.
> >
> > https://drive.google.com/file/d/0B_CbyhnbKqQDc2FaeWxITWxqdDg
> /view?usp=sharing
> >
> > Thanks,
> > Cheers,
> > Alex
> >
> > On Mon, Aug 15, 2016 at 2:52 PM, Szilárd Páll 
> > wrote:
> >
> >> Hi,
> >>
> >> Please post full logs; what you cut out of the file will often miss
> >> information needed to diagnose your issues.
> >>
> >> At first sight it seems that you simply have an imbalanced system. Not
> >> sure about the source of the imbalance and without knowing more about
> >> your system/setup and how is it decomposed what I can suggest is to:
> >> try other decomposition schemes or simply less decomposition (use more
> >> threads or less cores).
> >>
> >> Additionally you also have a pretty bad PP-PME load balance, but
> >> that's likely going to get better if you get you PP performance
> >> better.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >> On Sun, Aug 14, 2016 at 3:23 PM, Alexander Alexander
> >>  wrote:
> >> > Dear gromacs user,
> >> >
> >> > My free energy calculation works well, however, I am loosing around
> 56.5
> >> %
> >> > of the available CPU time as stated in my log file which is really
> >> > considerable. The problem is due to the load imbalance and domain
> >> > decomposition, but I have no idea to improve it, below is the very
> end of
> >> > my log file and I would be so appreciated if you could help avoid
> this.
> >> >
> >> >
> >> >D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
> >> >
> >> >  av. #atoms communicated per step for force:  2 x 115357.4
> >> >  av. #atoms communicated per step for LINCS:  2 x 2389.1
> >> >
> >> >  Average load imbalance: 285.9 %
> >> >  Part of the total run time spent waiting due to load imbalance: 56.5
> %
> >> >  Steps where the load balancing was limited by -rdd, -rcon and/or
> -dds:
> >> X 2
> >> > % Y 2 % Z 2 %
> >> >  Average PME mesh/force load: 0.384
> >> >  Part of the total run time spent waiting due to PP/PME imbalance:
> 14.5 %
> >> >
> >> > NOTE: 56.5 % of the available CPU time was lost due to load imbalance
> >> >   in the domain decomposition.
> >> >
> >> > NOTE: 14.5 % performance was lost because the PME ranks
> >> >   had less work to do than the PP ranks.
> >> >   You might want to decrease the number of PME ranks
> >> >   or decrease the cut-off and the grid spacing.
> >> >
> >> >
> >> >  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
> >> >
> >> > On 96 MPI ranks doing PP, and
> >> > on 32 MPI ranks doing PME
> >> >
> >> >  Computing:  Num   Num  CallWall time
>  Giga-Cycles
> >> >  Ranks Threads  Count  (s) total sum
>   %
> >> > 
> >> -
> >> >  Domain decomp.961 175000 242.339  53508.472
> >>  0.5
> >> >  DD comm. load 961 174903   9.076   2003.907
> >>  0.0
> >> >  DD comm. bounds   961 174901  27.054   5973.491
> >>  0.1
> >> >  Send X to PME 961701  44.342   9790.652
> >>  0.1
> >> >  Neighbor search   961 175001 251.994  55640.264
> >>  0.6
> >> >  Comm. coord.  96168250001521.009 335838.747
> >>  3.4
> >> >  Force 9617017001.9901546039.264
> >> 15.5
> >> >  Wait + Comm. F961701   10761.2962376093.759
> >> 23.8
> >> >  PME mesh *321701   11796.344 868210.788
> >>  8.7
> >> >  PME wait for PP *  22135.7521629191.096
> >> 16.3
> >> >  Wait 

Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[David van der Spoel]

On 16/08/16 09:28, Billy Williams-Noonan wrote:

Hi David,

   I was wondering if you had any advice on how to plot enthalpy against
COM pulling distance in the same manner that you have in *Figure 4* above?
Maybe I don't understand the question, but I'd say you just plot the 
potential energy (from the energy file) with error bar for each data 
point and normalize to zero at infinite distance.


   Best regards,

Billy

On 2 August 2016 at 18:15, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:


Yes we've noticed that.  Our error estimates for enthalpy are quite high
compared to the free energies at each umbrella window.

On 2 August 2016 at 17:10, David van der Spoel 
wrote:


On 20/07/16 02:51, Billy Williams-Noonan wrote:


Hi David,

  Thank you...!  To clarify, in Figure 4 of the paper referred to, you
seem
to have plotted the enthalpy of each frame against the COM pull distance
and then used those values and the PMFs at each point to compute -TdS ?
If
so I might do something similar.


Yes indeed.

The only problem is that enthalpies converge much more slowly than free
energies.



Billy

On Wednesday, 20 July 2016, David van der Spoel 
wrote:

On 19/07/16 12:22, Billy Williams-Noonan wrote:


Hi David,


  Thank you for all your responses on here. :)  We'll have to make you
an
author if/when this gets published haha.

   Will try to use gmx covar / anaeig at every point but my system has
30,000 atoms so it may not be completely faesible to get an accurate
value
for the system (same problem as before).

You only do this for the biomolecules separately, not the water.




   Could I simply use gmx energy and get an ensemble average enthalpy
for
each point?  Then I can use the Gibbs free energy equation to solve for
entropy.

Yes, this is what we did in the paper :).



Billy


On Tuesday, 19 July 2016, David van der Spoel 
wrote:

On 19/07/16 09:47, Billy Williams-Noonan wrote:



Hi All,



   I have seen papers where enthalpy and entropy are plotted against
the
distance of a steered MD pull and am wanting to do something similar.

   I have run a steered MD simulation pulling a cyclic peptide out of
the
binding site and the PMF calculation with *gmx wham* was in
reasonable
agreement with experiment.  to

We have published stuff like that (e.g. J. Chem. Theor. Comput. 9 pp.


4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)
There are two main ways of doing this, rerunning the PMF at different
temperatures and using the Van 't Hoff equation, or computing the
entropy
(approximately) using gmx covar / gmx anaeig for each of the species.

gmx sham is just for plotting an energy landscape, e.g.
J. Mol. Biol. 354 pp. 173-183 (2005)



   What I would like now is plot the entropy and enthalpy components


against the pull distance.  I stumbled across *gmx sham* and would
like
to
use that, however I can't find any information on how to use it
online.  I
found these posts on online forums but have found them to be
unhelpful
(I'm
sure it makes sense, it's just I am more of a chemist than a
mathematician).

*

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
hmlPKJSt/how-to-use-g-sham
<

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
hmlPKJSt/how-to-use-g-sham

*




*http://comments.gmane.org/gmane.science.biology.gromacs.user/64417
*

   Could someone please let me know the exact commands I need to use
with
*gmx
sham i*n order to plot entropy and enthalpy against the pull
distance?

   Kind regards,

Billy



--

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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send a mail to 

Re: [gmx-users] TPI and chemical potential

[Gmx QA]

Please - anyone?

I gathered from the mail-list that maybe the entire molecule (water in this
case) should be centered on origo (rather than having all atoms at (0,0,0),
but this gives me only a lot of inf for the chemical potential.

How can I calculate the excess chemical potential of water using TPI in
gromacs?



2016-08-15 13:31 GMT+02:00 Gmx QA :

> Dear list
>
> I am trying to teach myself how the test particle method for excess
> chemical potential calculations work. To this end, I created a small system
> of about 900 water molecules (TIP3p), and simulated for 1 ns.
>
> I then set up files for inserting an extra water molecule to calculate mu,
> the chemical potential.
>
> The end of my tpi_start.gro looks like this:
> 
>   884SOL OW 2650   2.466   0.788   2.747 -0.5599 -0.0387  0.0570
>   884SOLHW1 2651   2.529   0.835   2.802  0.0024 -0.9901  0.2261
>   884SOLHW2 2652   2.506   0.703   2.732 -1.4472 -0.3598 -0.5022
>   885SOL OW 2653   0.000   0.000   0.000  0.  0.  0.
>   885SOLHW1 2654   0.000   0.000   0.000  0.  0.  0.
>   885SOLHW2 2655   0.000   0.000   0.000  0.  0.  0.
>3.01188   3.01188   3.01188
>
> So I think this last water molecule is the one to be inserted. The
> topology was also updated accordingly.
>
> I then made a rerun like this:
>
> $ gmx mdrun -v -deffnm tpi -rerun md.xtc
>
> And the output is a series of lines like this:
>
> Reading frame 180 time  900.000   mu  8.924e+00   7.240e+00
> mu  7.671e+00   7.242e+00
> mu  6.987e+00   7.241e+00
> mu  7.010e+00   7.239e+00
> mu  7.691e+00   7.241e+00
> mu  7.439e+00   7.242e+00
> mu  6.757e+00   7.240e+00
> mu  8.114e+00   7.243e+00
> mu  7.173e+00   7.243e+00
> mu  8.768e+00   7.249e+00
> Reading frame 190 time  950.000   mu  7.799e+00   7.252e+00
> mu  9.284e+00   7.259e+00
> mu  8.103e+00   7.262e+00
> mu  7.835e+00   7.265e+00
> mu  7.321e+00   7.265e+00
> mu  7.576e+00   7.267e+00
> mu  9.348e+00   7.274e+00
> mu  7.021e+00   7.272e+00
> mu  7.162e+00   7.272e+00
> mu  7.695e+00   7.274e+00
> Reading frame 200 time 1000.000   mu  7.104e+00   7.273e+00
>
> Now, is  here the average computed chemical potential? What is the TPI
> energy distribution being reported in the tpi.xvg-file?
>
> I tried to google for the chemical potential of water and according to
> e.g. [1] (page 13) it should be around -23.5 kJ/mol. I would really
> appreciate if someone could comment on this, as I need to understand it
> before moving on to more relevant (for me) systems….
>
> Thanks
> /PK
>
>
>
>
>
> [1] Chemical potential of liquids and mixtures via Adaptive Resolution ...
> 
>
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Re: [gmx-users] Generating Entropy from Umbrella Sampling Data

[Billy Williams-Noonan]

Hi David,

   I was wondering if you had any advice on how to plot enthalpy against
COM pulling distance in the same manner that you have in *Figure 4* above?

   Best regards,

Billy

On 2 August 2016 at 18:15, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Yes we've noticed that.  Our error estimates for enthalpy are quite high
> compared to the free energies at each umbrella window.
>
> On 2 August 2016 at 17:10, David van der Spoel 
> wrote:
>
>> On 20/07/16 02:51, Billy Williams-Noonan wrote:
>>
>>> Hi David,
>>>
>>>   Thank you...!  To clarify, in Figure 4 of the paper referred to, you
>>> seem
>>> to have plotted the enthalpy of each frame against the COM pull distance
>>> and then used those values and the PMFs at each point to compute -TdS ?
>>> If
>>> so I might do something similar.
>>>
>> Yes indeed.
>>
>> The only problem is that enthalpies converge much more slowly than free
>> energies.
>>
>>
>>> Billy
>>>
>>> On Wednesday, 20 July 2016, David van der Spoel 
>>> wrote:
>>>
>>> On 19/07/16 12:22, Billy Williams-Noonan wrote:

 Hi David,
>
>   Thank you for all your responses on here. :)  We'll have to make you
> an
> author if/when this gets published haha.
>
>Will try to use gmx covar / anaeig at every point but my system has
> 30,000 atoms so it may not be completely faesible to get an accurate
> value
> for the system (same problem as before).
>
> You only do this for the biomolecules separately, not the water.


>Could I simply use gmx energy and get an ensemble average enthalpy
> for
> each point?  Then I can use the Gibbs free energy equation to solve for
> entropy.
>
> Yes, this is what we did in the paper :).


 Billy
>
> On Tuesday, 19 July 2016, David van der Spoel 
> wrote:
>
> On 19/07/16 09:47, Billy Williams-Noonan wrote:
>
>>
>> Hi All,
>>
>>>
>>>I have seen papers where enthalpy and entropy are plotted against
>>> the
>>> distance of a steered MD pull and am wanting to do something similar.
>>>
>>>I have run a steered MD simulation pulling a cyclic peptide out of
>>> the
>>> binding site and the PMF calculation with *gmx wham* was in
>>> reasonable
>>> agreement with experiment.  to
>>>
>>> We have published stuff like that (e.g. J. Chem. Theor. Comput. 9 pp.
>>>
>> 4542-4551 (2013)http://pubs.acs.org/doi/abs/10.1021/ct400404q)
>> There are two main ways of doing this, rerunning the PMF at different
>> temperatures and using the Van 't Hoff equation, or computing the
>> entropy
>> (approximately) using gmx covar / gmx anaeig for each of the species.
>>
>> gmx sham is just for plotting an energy landscape, e.g.
>> J. Mol. Biol. 354 pp. 173-183 (2005)
>>
>>
>>
>>What I would like now is plot the entropy and enthalpy components
>>
>>> against the pull distance.  I stumbled across *gmx sham* and would
>>> like
>>> to
>>> use that, however I can't find any information on how to use it
>>> online.  I
>>> found these posts on online forums but have found them to be
>>> unhelpful
>>> (I'm
>>> sure it makes sense, it's just I am more of a chemist than a
>>> mathematician).
>>>
>>> *
>>>
>>> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
>>> hmlPKJSt/how-to-use-g-sham
>>> <
>>>
>>> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/
>>> hmlPKJSt/how-to-use-g-sham
>>>
>>> *


>>> *http://comments.gmane.org/gmane.science.biology.gromacs.user/64417
>>> >> >*
>>>
>>>I have also looked through the Gromacs 5.1.2 manual and cannot
>>> find
>>> anything on *gmx sham*.
>>>
>>> *http://manual.gromacs.org/documentation/5.1.2/manual-5.1.2.pdf
>>> *
>>>
>>>Could someone please let me know the exact commands I need to use
>>> with
>>> *gmx
>>> sham i*n order to plot entropy and enthalpy against the pull
>>> distance?
>>>
>>>Kind regards,
>>>
>>> Billy
>>>
>>>
>>>
>>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>> --
>> 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
>> 

[gmx-users] Correction for the use of harmonic position restraints in Umbrella Sampling

[Billy Williams-Noonan]

Hi Gromacs Experts,

   I have generated some binding free energies using steered MD and
umbrella sampling.  I've done this using a variation of the method
described by Justin Lemkul in his tutorial.

   My question is this:  do I have to correct my PMF dG calculation for the
use of position restraints, or does *gmx wham* already take this into
account?  My dG values are consistently higher than experimental values so
I was hoping this could help explain why.

   Best regards,

Billy

-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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