date:20130731

[gmx-users] vdwtype in mdp file for LIE method

2013-07-31 Thread Mahboobeh Eslami

hi all freind
what is vdwtype in mdp file for LIE method in free energy calculation?
best regard
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[gmx-users] Umbrella Sampling

2013-07-31 Thread Steven Neumann

Dear Gmx Users,

I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.

I pulled my molecule away and two ions were also detached from the protein
surface being attached to my ligand.

My question: if I run my US caluclation and combine windows by WHAM (I
specified in my umbrella.mdp my ligand as a pull_group1 and same protein
residues I pulled it from as pull_group0) will get the PMF profile for my
ligand binding or ligand and two ions binding?

Steven
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread David van der Spoel


On 2013-07-31 07:20, bipin singh wrote:

Hello All,

I was trying to do clustering on my MD trajectory using gromos method under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the output
gives a single cluster. Please let me know if I have not understood it
correctly.


It means everything is within 0.3 nm RMSD from each other. Maybe your 
system is very stable or you did not simulate very long. You can use a 
shorter cut-off.


I am appending the output below:


Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
##




--
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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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread bipin singh

Thanks for the reply Prof. David. But in the output it shows that "The RMSD
ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
me. So I think it should write the snapshots having RMSD greater than 0.3nm
(cutoff) to another cluster.


On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
wrote:

> On 2013-07-31 07:20, bipin singh wrote:
>
>> Hello All,
>>
>> I was trying to do clustering on my MD trajectory using gromos method
>> under
>> g_cluster module. I got one doubt regarding the output, as I used the
>> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
>> snapshots which have RMSD less than or equal to 0.3nm will form the first
>> cluster and the rest of snapshots will form another cluster. But the
>> output
>> gives a single cluster. Please let me know if I have not understood it
>> correctly.
>>
>
> It means everything is within 0.3 nm RMSD from each other. Maybe your
> system is very stable or you did not simulate very long. You can use a
> shorter cut-off.
>
>
>> I am appending the output below:
>>
>> ##**##
>> Using gromos method for clustering
>> Using RMSD cutoff 0.3 nm
>> The RMSD ranges from 0.0602553 to 0.411066 nm
>> Average RMSD is 0.107366
>> Number of structures for matrix 12501
>> Energy of the matrix is 960.075 nm
>>
>> Found 1 clusters
>>
>> Writing middle structure for each cluster to clusters.pdb
>> Counted 0 transitions in total, max 0 between two specific clusters
>> ##**
>>
>>
>
> --
> 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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Re: [gmx-users] vdwtype in mdp file for LIE method

2013-07-31 Thread Mark Abraham

What does your background reading suggest is a good choice for VDW type?

Mark

On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami
 wrote:
> hi all freind
> what is vdwtype in mdp file for LIE method in free energy calculation?
> best regard
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread David van der Spoel


On 2013-07-31 09:45, bipin singh wrote:

Thanks for the reply Prof. David. But in the output it shows that "The RMSD
ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
me. So I think it should write the snapshots having RMSD greater than 0.3nm
(cutoff) to another cluster.
I see, then maybe the definition is different (check the source code!). 
It could be that it is 0.3 nm from the cluster center.



On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
wrote:


On 2013-07-31 07:20, bipin singh wrote:


Hello All,

I was trying to do clustering on my MD trajectory using gromos method
under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the
output
gives a single cluster. Please let me know if I have not understood it
correctly.



It means everything is within 0.3 nm RMSD from each other. Maybe your
system is very stable or you did not simulate very long. You can use a
shorter cut-off.



I am appending the output below:

##**##
Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
##**




--
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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 posting!
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--
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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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread Tsjerk Wassenaar

Hi Bipin,

If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll
end up in the same cluster.

Cheers,

Tsjerk


On Wed, Jul 31, 2013 at 9:45 AM, bipin singh  wrote:

> Thanks for the reply Prof. David. But in the output it shows that "The RMSD
> ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
> me. So I think it should write the snapshots having RMSD greater than 0.3nm
> (cutoff) to another cluster.
>
>
> On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
> wrote:
>
> > On 2013-07-31 07:20, bipin singh wrote:
> >
> >> Hello All,
> >>
> >> I was trying to do clustering on my MD trajectory using gromos method
> >> under
> >> g_cluster module. I got one doubt regarding the output, as I used the
> >> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
> >> snapshots which have RMSD less than or equal to 0.3nm will form the
> first
> >> cluster and the rest of snapshots will form another cluster. But the
> >> output
> >> gives a single cluster. Please let me know if I have not understood it
> >> correctly.
> >>
> >
> > It means everything is within 0.3 nm RMSD from each other. Maybe your
> > system is very stable or you did not simulate very long. You can use a
> > shorter cut-off.
> >
> >
> >> I am appending the output below:
> >>
> >> ##**##
> >> Using gromos method for clustering
> >> Using RMSD cutoff 0.3 nm
> >> The RMSD ranges from 0.0602553 to 0.411066 nm
> >> Average RMSD is 0.107366
> >> Number of structures for matrix 12501
> >> Energy of the matrix is 960.075 nm
> >>
> >> Found 1 clusters
> >>
> >> Writing middle structure for each cluster to clusters.pdb
> >> Counted 0 transitions in total, max 0 between two specific clusters
> >> ##**
> >>
> >>
> >
> > --
> > 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
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
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> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> >
>
>
>
> --
> *---
> Thanks and Regards,
> Bipin Singh*
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
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Re: [gmx-users] Regarding gromos method in g_cluster

2013-07-31 Thread bipin singh

Now got the point. Thank you Tsjerk Sir and Prof. David for the help.


On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar  wrote:

> Hi Bipin,
>
> If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll
> end up in the same cluster.
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, Jul 31, 2013 at 9:45 AM, bipin singh  wrote:
>
> > Thanks for the reply Prof. David. But in the output it shows that "The
> RMSD
> > ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to
> > me. So I think it should write the snapshots having RMSD greater than
> 0.3nm
> > (cutoff) to another cluster.
> >
> >
> > On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel
> > wrote:
> >
> > > On 2013-07-31 07:20, bipin singh wrote:
> > >
> > >> Hello All,
> > >>
> > >> I was trying to do clustering on my MD trajectory using gromos method
> > >> under
> > >> g_cluster module. I got one doubt regarding the output, as I used the
> > >> cutoff of 0.3nm for RMSD calculation, I was expecting that all the
> > >> snapshots which have RMSD less than or equal to 0.3nm will form the
> > first
> > >> cluster and the rest of snapshots will form another cluster. But the
> > >> output
> > >> gives a single cluster. Please let me know if I have not understood it
> > >> correctly.
> > >>
> > >
> > > It means everything is within 0.3 nm RMSD from each other. Maybe your
> > > system is very stable or you did not simulate very long. You can use a
> > > shorter cut-off.
> > >
> > >
> > >> I am appending the output below:
> > >>
> > >> ##**##
> > >> Using gromos method for clustering
> > >> Using RMSD cutoff 0.3 nm
> > >> The RMSD ranges from 0.0602553 to 0.411066 nm
> > >> Average RMSD is 0.107366
> > >> Number of structures for matrix 12501
> > >> Energy of the matrix is 960.075 nm
> > >>
> > >> Found 1 clusters
> > >>
> > >> Writing middle structure for each cluster to clusters.pdb
> > >> Counted 0 transitions in total, max 0 between two specific clusters
> > >> ##**
> > >>
> > >>
> > >
> > > --
> > > 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
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > * Please search the archive at http://www.gromacs.org/**
> > > Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >
> >
> >
> >
> > --
> > *---
> > Thanks and Regards,
> > Bipin Singh*
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] probabilty density of C5-C6 bond of all DNA conformer

2013-07-31 Thread Collins Nganou

Dear Users,

I am looking the way to extract the probability density of the C5-C6.
I will be very grateful to receive an indication on how to monitor it.

Best regards

Collins
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Aw: [gmx-users] Umbrella Sampling

2013-07-31 Thread lloyd riggs

>will get the PMF profile for my
>ligand binding or ligand and two ions binding?

It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation?

Gesendet: Mittwoch, 31. Juli 2013 um 09:29 Uhr
Von: "Steven Neumann"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] Umbrella Sampling

Dear Gmx Users,

I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.

I pulled my molecule away and two ions were also detached from the protein
surface being attached to my ligand.

My question: if I run my US caluclation and combine windows by WHAM (I
specified in my umbrella.mdp my ligand as a pull_group1 and same protein
residues I pulled it from as pull_group0) will get the PMF profile for my
ligand binding or ligand and two ions binding?

Steven
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[gmx-users] topology and coordinate file not matching after grompp

2013-07-31 Thread chinnu657

Hello,

I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.

Basically, I am trying to mix 2 different proteins in one box and after
doing my grompp to neutralise the system, I get the error number of
coordinates in coordinate file (solvated.gro, 85059) does not match topology
(topol.top, 85079).

This is how my topology file looks:
;GROMACS toplogy

;
;Include the force field
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "topol_1AKI.itp"
#include "topol_2CDS.itp"

;Include water topology
#include "spce.itp"

;Include generic ion topology
#include "ions.itp"

[ system ]
Two proteins in water

[ molecules ]
Protein_1AKI1
Protein_2CDS1
SOL 27053

How can I deduce from this data that the number of coordinates in topol.top
is 85079. And what exactly should I do to reduce the number of molecules
here so that the 2 files have the same number of coordinates.

I will really appreciate the help. I am pretty new with MD simulations

Kind Regards,
Chinnu

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Re: [gmx-users] Umbrella Sampling

2013-07-31 Thread Steven Neumann

They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this group included.


On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs  wrote:

>
> >will get the PMF profile for my
> >ligand binding or ligand and two ions binding?
>
> It would be the ligand and two ions unless the ions also at some point
> discossiate from the ligand once in solvent. Could add positional restraint
> for them, but dont know how that effects the calculation?
>  *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
> *Von:* "Steven Neumann" 
> *An:* "Discussion list for GROMACS users" 
> *Betreff:* [gmx-users] Umbrella Sampling
> Dear Gmx Users,
>
> I run SMD to extract the windows for US calculations. The system involves
> negatively charged ligand and protein. I generated the protein-ligand
> complex within self assembly MD simulations.
>
> I pulled my molecule away and two ions were also detached from the protein
> surface being attached to my ligand.
>
> My question: if I run my US caluclation and combine windows by WHAM (I
> specified in my umbrella.mdp my ligand as a pull_group1 and same protein
> residues I pulled it from as pull_group0) will get the PMF profile for my
> ligand binding or ligand and two ions binding?
>
> Steven
> --
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Re: [gmx-users] Umbrella Sampling

2013-07-31 Thread Steven Neumann

But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would Justin
please comment on this?


On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann wrote:

> They do not dissociate...Are you sure? My mdp specifies only ligand as a
> pull_group1. I think it would change having ions in this group included.
>
>
> On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs  wrote:
>
>>
>> >will get the PMF profile for my
>> >ligand binding or ligand and two ions binding?
>>
>> It would be the ligand and two ions unless the ions also at some point
>> discossiate from the ligand once in solvent. Could add positional restraint
>> for them, but dont know how that effects the calculation?
>>  *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
>> *Von:* "Steven Neumann" 
>> *An:* "Discussion list for GROMACS users" 
>> *Betreff:* [gmx-users] Umbrella Sampling
>> Dear Gmx Users,
>>
>> I run SMD to extract the windows for US calculations. The system involves
>> negatively charged ligand and protein. I generated the protein-ligand
>> complex within self assembly MD simulations.
>>
>> I pulled my molecule away and two ions were also detached from the protein
>> surface being attached to my ligand.
>>
>> My question: if I run my US caluclation and combine windows by WHAM (I
>> specified in my umbrella.mdp my ligand as a pull_group1 and same protein
>> residues I pulled it from as pull_group0) will get the PMF profile for my
>> ligand binding or ligand and two ions binding?
>>
>> Steven
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[gmx-users] umbrella Sampling and PMF- Error estimation

2013-07-31 Thread Mohsen Ramezanpour

Hi everyone

How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?

Actually I did an umbrella sampling for protein and ligand complex and
I have a PMF profile now but I do not know how much is my error!


Thanks in advance for any suggestion
Mohsen
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