Re: [gmx-users] generating martini-version of lipids

[jagannath mondal]

Hi Tsjerk
  Thanks for your response. I was mainly looking for converting a dppg
bilayer in charm36 format into a coarse-grained one. However, the "Mapping"
folder does not have any mapping for dppg lipids. Is there any specific
suggestion regarding this?
Jagannath

On Mon, Feb 29, 2016 at 10:10 PM, Tsjerk Wassenaar 
wrote:

> Hi Jagannath,
>
> Backward actually can do both. For conversion of a Gromos system use
>
> backward.py -from gromos -to martini
>
> Hope it helps,
>
> Tsjerk
>
>
> On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal <
> jmondal.bac...@gmail.com
> > wrote:
>
> > Dear Gromacs/Martini-users
> >
> > I wanted to transform a snapshot of my atomistic DPPG/water bilayer to
> the
> > Martini coarse-grained format. However, I found martinize.py script  does
> > not transform lipid or waters to coarse-grained counterpart.It only works
> > for protein. So, Is there any particular way I can generate the CG
> version
> > of my atomistic DPPG/water bilayer ?
> >
> > I guess backward scripts does the reverse of what I am trying to achieve.
> > So, if you can suggest a way to generate a coarse-grained pdb files of
> the
> > atomistic lipid bilayer/water, that will be very helpful.
> >
> > Jagannath
> > --
> > Gromacs Users mailing list
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

Thanks Peter, I thought as much. At the time it just seemed like an odd
bit of information to report.

Many thanks
Anthony 

Dr Anthony Nash
Department of Chemistry
University College London





On 01/03/2016 03:15, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Peter Stern"  wrote:

>This is a non-problem.  You will never get zero eigenvalues for such a
>large system since you are not at an absolute minimum.  The fact that you
>got no negative eigenvalues and the six lowest eigenvalues are very small
>(surely much, much smaller than the subsequent eigenvalues) indicates
>that you are at a reasonably good minimum. But don't be misled. Another
>(different) minimization could bring the system to a different minimum
>(also good) with somewhat different eigenvalues and eigenvectors.
>
>Regards,
>Peter Stern
>
>Sent from my iPhone
>
>> On 29 Feb 2016, at 3:23 PM, Nash, Anthony  wrote:
>> 
>> Hi all,
>> 
>> Hoping this will be the final stumbling block. I’ve successfully
>>minimised
>> my structure to a a very small max force:
>> Potential Energy  = -1.93736854460113e+03
>> Maximum force =  7.39399083846082e-04 on atom 34
>> Norm of force =  1.64068483698544e-04
>> 
>> 
>> When I perform integrator=nm there are no warning of potential imaginary
>> (negative) values. However, upon running:
>> g_nmeig_d -f dogdic_nma.mtx -s dogdic_nma.tpr -last 3000
>> I see the following:
>> 
>> 
>> 
>> Full matrix storage format, nrow=279, ncols=279
>> Diagonalizing to find vectors 1 through 279...
>> 
>> One of the lowest 6 eigenvalues has a non-zero value.
>> 
>> This could mean that the reference structure was not
>> properly energy minimized.
>> Writing eigenvalues...
>> 
>> Back Off! I just backed up eigenval.xvg to ./#eigenval.xvg.2#
>> Writing eigenfrequencies - negative eigenvalues will be set to zero.
>> 
>> 
>> 
>> 
>> My lowest 6 eigenvalues are:
>> 1   0.0780823
>> 20.153357
>> 30.174772
>> 40.327362
>> 50.466203
>> 6 0.64693
>> 
>> 
>> I’m a little confused by the statement "One of the lowest 6 eigenvalues
>> has a non-zero value. This could mean that the reference structure was
>>not
>> properly energy minimized.” Really? Surely it out to be if one or more
>>of
>> the values is negative.  Also, there were no eigenvalues set to zero
>> (hence, I can only assume I have no negative eigenvalues).
>> 
>> Would appreciate a little insight.
>> Many thanks
>> Anthony
>> 
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>> 
>> 
>> 
>> 
>> 
>> On 29/02/2016 16:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Nash, Anthony"
>> > a.n...@ucl.ac.uk> wrote:
>> 
>>> Dear Mark and Justin,
>>> 
>>> By removing the restraints (your suggestions) it appears to have
>>>worked!
>>> 
>>> Maximum force: 9.21098e-04
>>> Writing Hessian...
>>> 
>>> This now matches the same force as my energy minimisation. Many thanks
>>>for
>>> you help.
>>> 
>>> Thanks
>>> Anthony
>>> 
>>> 
>>> 
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 29/02/2016 14:46,
>>>"gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>>> behalf of Mark Abraham"
>>>>> on behalf of mark.j.abra...@gmail.com> wrote:
>>> 
 Hi,
 
 An earlier mdp file suggested you were using position restraints.
There
 should be no need for this, nor any problem, but what happens without
 them?
 
 Mark
 
> On Mon, 29 Feb 2016 15:39 Nash, Anthony  wrote:
> 
> Hi Justin,
> 
> After some digging I had found that link and made some adjustments
>(as
> presented in the later email).
> 
> After a series of energy minimisations (including switching LINCS
>off,
> and
> dropping the energy step to a very small number), and with the final
> command:
> grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
> modic_cg_3.trr
> 
> 
> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883
> steps
> Potential Energy  = -1.92681826422996e+03
> Maximum force =  8.54361662283108e-04 on atom 44
> Norm of force =  2.71110116926712e-04
> 
> 
> However, when switching to integrator=nm, running grompp_d -f nma.mdp
> -c
> modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
> mdrun_d, I get:
> 
> Maximum force: 5.19179e+01
> The force is probably not small enough to ensure that you are at a
> minimum.
> Be aware that negative eigenvalues may occur
> when the resulting matrix is diagonalized.

[gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer

[kamakshi sikka]

Hello everyone,


I want to calculate deuterium order parameter for 25POPC/103POPS mixed
lipid bilayer. But, I don't know how to make index groups for sn1 and sn2
acyl chains for both POPS and POPC lipids separately.
Please help.

Regards
Kamakshi
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Re: [gmx-users] Sulfate ion parameters

[#SUKRITI GUPTA#]

Dear Mark,

Thanks for the reply. Actually, I emailed the corresponding author but didn't 
get any reply. Also, it is not mentioned in the paper that the model is for a 
rigid system.

Regards
Sukriti


Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg





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

Sent: Monday, February 29, 2016 7:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Sulfate ion parameters

Hi,

Such questions are why all published articles list the email address of a
"corresponding author" ;-) But first, be sure their model wasn't designed
to be rigid, and so have no internal parameters such as you are seeking.

Mark

On Mon, Feb 29, 2016 at 12:01 PM #SUKRITI GUPTA# 
wrote:

> Thanks for the reply.
>
> I got one paper stating non bonded parameter values for sulphate ions:
> "Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic
> Properties", but this paper does not provide bonded parameters required for
> simulating sulfate ions, i.e. bond bending and stretching parameters. Is
> there a way to find what parameters were used in the study.
>
> Thanks and Regards
> Sukriti
>
>
>
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N)
> | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christian
> Bope Domilongo 
> Sent: Wednesday, February 24, 2016 4:43 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Sulfate ion parameters
>
> You may try to generate topology file using Topolbuilder
> http://www.gromacs.org/Downloads/User_contributions/Other_software
> Regards,
>
>
> On 24 February 2016 at 14:16, #SUKRITI GUPTA# 
> wrote:
>
> > Dear gromacs users,
> >
> >
> > I wanted to simulate sulphate ions in water using oplsaa force field but
> I
> > couldn't find parameters for sulphur and oxygen atoms of sulphate ions in
> > the oplsaa force field files. Can anyone suggest from where can I get
> these
> > parameters?
> >
> >
> > Charmm force field has the parameters for sulphate ions, so is it
> possible
> > to use those parameters itself for simulations? Also the partial charges
> > given in charmm force field to S and O of sulphate ions do not add up to
> > -2. (S +1.33, O -0.78) So how to select the correct partial charges here?
> >
> >
> > Thanks and Regards
> >
> > Sukriti
> >
> >
> > [
> >
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3
> > ]
> >
> > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N
> )
> > | Nanyang Technological University
> > N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> > Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:
> > erian.ntu.edu.sg
> >
> >
> >
> > --
> > 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.
> >
>
>
>
> --
> Bope Domilongo Christian
> Ph.D candidate in Computational Biology
> Division of Structural Biology and Biochemistry
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> +6590565804
> http://www.ntu.edu.sg/
> --
> Gromacs Users mailing list
>
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> posting!
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> 

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Peter Stern]

This is a non-problem.  You will never get zero eigenvalues for such a large 
system since you are not at an absolute minimum.  The fact that you got no 
negative eigenvalues and the six lowest eigenvalues are very small (surely 
much, much smaller than the subsequent eigenvalues) indicates that you are at a 
reasonably good minimum. But don't be misled. Another (different) minimization 
could bring the system to a different minimum (also good) with somewhat 
different eigenvalues and eigenvectors.

Regards,
Peter Stern

Sent from my iPhone

> On 29 Feb 2016, at 3:23 PM, Nash, Anthony  wrote:
> 
> Hi all,
> 
> Hoping this will be the final stumbling block. I’ve successfully minimised
> my structure to a a very small max force:
> Potential Energy  = -1.93736854460113e+03
> Maximum force =  7.39399083846082e-04 on atom 34
> Norm of force =  1.64068483698544e-04
> 
> 
> When I perform integrator=nm there are no warning of potential imaginary
> (negative) values. However, upon running:
> g_nmeig_d -f dogdic_nma.mtx -s dogdic_nma.tpr -last 3000
> I see the following:
> 
> 
> 
> Full matrix storage format, nrow=279, ncols=279
> Diagonalizing to find vectors 1 through 279...
> 
> One of the lowest 6 eigenvalues has a non-zero value.
> 
> This could mean that the reference structure was not
> properly energy minimized.
> Writing eigenvalues...
> 
> Back Off! I just backed up eigenval.xvg to ./#eigenval.xvg.2#
> Writing eigenfrequencies - negative eigenvalues will be set to zero.
> 
> 
> 
> 
> My lowest 6 eigenvalues are:
> 1   0.0780823
> 20.153357
> 30.174772
> 40.327362
> 50.466203
> 6 0.64693
> 
> 
> I’m a little confused by the statement "One of the lowest 6 eigenvalues
> has a non-zero value. This could mean that the reference structure was not
> properly energy minimized.” Really? Surely it out to be if one or more of
> the values is negative.  Also, there were no eigenvalues set to zero
> (hence, I can only assume I have no negative eigenvalues).
> 
> Would appreciate a little insight.
> Many thanks
> Anthony
> 
> Dr Anthony Nash
> Department of Chemistry
> University College London
> 
> 
> 
> 
> 
> On 29/02/2016 16:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Nash, Anthony"
>  a.n...@ucl.ac.uk> wrote:
> 
>> Dear Mark and Justin,
>> 
>> By removing the restraints (your suggestions) it appears to have worked!
>> 
>> Maximum force: 9.21098e-04
>> Writing Hessian...
>> 
>> This now matches the same force as my energy minimisation. Many thanks for
>> you help.
>> 
>> Thanks
>> Anthony
>> 
>> 
>> 
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>> 
>> 
>> 
>> 
>> 
>> On 29/02/2016 14:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>> behalf of Mark Abraham" > on behalf of mark.j.abra...@gmail.com> wrote:
>> 
>>> Hi,
>>> 
>>> An earlier mdp file suggested you were using position restraints. There
>>> should be no need for this, nor any problem, but what happens without
>>> them?
>>> 
>>> Mark
>>> 
 On Mon, 29 Feb 2016 15:39 Nash, Anthony  wrote:
 
 Hi Justin,
 
 After some digging I had found that link and made some adjustments (as
 presented in the later email).
 
 After a series of energy minimisations (including switching LINCS off,
 and
 dropping the energy step to a very small number), and with the final
 command:
 grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
 modic_cg_3.trr
 
 
 Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883
 steps
 Potential Energy  = -1.92681826422996e+03
 Maximum force =  8.54361662283108e-04 on atom 44
 Norm of force =  2.71110116926712e-04
 
 
 However, when switching to integrator=nm, running grompp_d -f nma.mdp
 -c
 modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
 mdrun_d, I get:
 
 Maximum force: 5.19179e+01
 The force is probably not small enough to ensure that you are at a
 minimum.
 Be aware that negative eigenvalues may occur
 when the resulting matrix is diagonalized.
 
 
 
 I¹m still struggling to yield a maximum force during the integrator=nm
 step, as presented from the earlier cg step. The .mdp files are
 identical
 with the exception of the integrator line.
 
 Thanks
 Anthony
 
 
 Dr Anthony Nash
 Department of Chemistry
 University College London
 
 
 
 
 
 On 29/02/2016 12:49, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 on
 behalf of Justin Lemkul"
 

Re: [gmx-users] creating representative structures

[Shyno Mathew]

Dear all,

I was able to write a tcl script to do cluster analysis, here I am using
the gromos method.
However, my script is giving slightly different results! I am testing my
script on a smaller trajectory (8 frames).
In the gromos method, the structure with the greatest number of neighbors
is considered as the center of the cluster.
What if more than one structure has the highest number of neighbors. For
example, in my calculation, both frames 4 and 6 has 6 neighbors (maximum
neighbor count).
When I used g_cluster, the output file shows cluster center as frame 6.
That means if I have more than one structure that has the maximum number of
neighbors, I can randomly choose the cluster center?

thanks,
Shyno


On Fri, Feb 26, 2016 at 11:47 AM, Shyno Mathew  wrote:

> Dear Prof. Mark and Prof. Stephane,
>
> Thanks so much for your suggestions.
>
> thanks,
> Shyno
>
> On Mon, Feb 8, 2016 at 12:23 PM, Shyno Mathew  wrote:
>
>> Dear all,
>>
>>
>> I have few questions regarding creating representative structures. For
>> simplicity, let’s say I have a trajectory of 5 frames:
>>
>> 1.   g_rmsf: After reading previous posts, here is what I
>> understood. The average structures calculated using g_rmsf (by specifying
>> –ox) is literally the average of x, y, z co-ordinates of each atom over all
>> the 5 frames in my case. Energy minimizing this averaged structure might
>> give a meaningful structure?
>>
>> 2.   g_cluster: Here I am using the gromos method. I read the
>> reference paper (Daura et al.). Using gromos method and by just specifying
>> –cl (not –av) I get the middle structures for each cluster. Let’s say I get
>> 2 clusters using rmsd 0.16. Now the representative structures of these two
>> clusters (obtained in the out.pdb) should exactly correspond to two frames
>> in my original trajectory (the one with 5 frames)?
>>
>> 3.   My final question is regarding how exactly g_cluster works,
>> here is what I understand from Daura et al.
>>
>> If I use g_cluster with gromos method, the code will look for neighbors
>> of each frame within specified cutoff.
>>
>> Assume the first time the code finds the following:
>>
>> frame 0 has two neighbors: frames 2,3  within cutoff
>>
>> frame 1 has three neighbors: frames 2, 3, 4 within cutoff
>>
>> frame 2 has four neighbors: frames 0, 1, 3, 4 within cutoff
>>
>> frame 3 has three neighbors: frames 0,1, 2 within cutoff
>>
>> frame 4 has two neighbors: frames 1,2 within cutoff
>>
>>
>>
>> Since frame 2 has the highest number of neighbors, it's considered the
>> center cluster and this frame along with neighbors are removed. The same
>> calculation is performed on the remaining frames if I had more frames.
>>
>>
>>
>> Thanks in advance for your help,
>>
>> Sincerely,
>>
>> Shyno
>>
>> --
>> Shyno Mathew
>> PhD Candidate
>> Department of Chemical Engineering
>> Graduate Assistant
>> Office of Graduate Student Affairs
>> The Fu Foundation School Of Engineering and Applied Science
>> Columbia University
>>
>
>
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>



-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University
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Re: [gmx-users] Calculate energy associated with hydrogen bond

[Erik Marklund]

Hi,

This paper might be helpful 
https://www.researchgate.net/publication/222873041_Hydrogen_bond_strengths_revealed_by_topological_analyses_of_experimentally_observed_electron_densities_Chem_Phys_Lett.
 But you would need to know which is donor and acceptor, and which hydrogen. 
But that you can get from g_hbond.

Kind regards,
Erik

On 29 Feb 2016, at 19:20, Tushar Ranjan Moharana 
> wrote:

Hi Everyone,
Can anyone let me know how to calculate energy associated with hydrogen
bond? Particularly if I am not sure which one is the acceptor (or donor) or
there is a probability of more than one acceptor for a given donor or vice
versa.

Thanks a lot.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] Coarse grain membrane simulation of DPPC

[Tsjerk Wassenaar]

Hi Ali,

Coarse grain and atomistic system probably respond differently to high
pressures.

Cheers,

Tsjerk
On Feb 29, 2016 21:23,  wrote:

>
>
>
>
> Dear all
>
>
> Recently I saw  an article about 128DPPC  of lipid bilayer. it
> says that the bilayer would rupture by a
> lateral 200bar tension, using Gromacs all atom. now I want to gain that
> using coarsegrain method. for all atom the pdb file is obtainable but for
> CG, I built it using :
>
>
> python insane.py -l DPPC -x 6 -y 6 -z 7.498 -pbc cubic -sol w -o
> dppc.gro
> -p system.top
>
>
> I do minimization and NPT equilibrium. but when I load it with
> 200bar or
> even 100 bar the system fail less than 1ns but the article gain for 200
> bar, a time period of 8ns  and for 100 bar, no pore formation. oddly
> when I load it with 50bar I can elicit the correct answer for Area per
> lipid for the example.( I obtain 0.74 which is ok based on the
> article)
>
>
> any comment on where probably I was wrong ? I really apreciate it.
>
>
> best regards
>
>
> Ali
>
>
> ==
>
>
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
>
>
> Department of Mechanical Engineering
>
>
> Sharif University of Technology, Tehran, Iran
>
>
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[gmx-users] No bonds in *.top file

[Dawid das]

Dear Gromacs Experts,

I run gmx pdb2gmx and it runs without any warnings or errors by the *.top
file does not
contain any bonds. The *.gro file is fine and all hydrogen atoms are added
correctly.

Now I have discovered that when I get rid of calcium ions in my *.pdb file
I get proper
*.top file. But I don't want to get rid of them. How can I generate proper
*.top file
with my Calcium ions?
They are orginally part of the same chain (A) as the protein and water
molecules.
When I changes this to B chain (calcium ions) it does not help.

Best wishes,
Dawid Grabarek
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[gmx-users] Coarse grain membrane simulation of DPPC

[khourshaeishargh]

Dear all


Recently I saw� an article about 128DPPC� of lipid bilayer. it says 
that the bilayer would rupture by a
lateral 200bar tension, using Gromacs all atom. now I want to gain that
using coarsegrain method. for all atom the pdb file is obtainable but for
CG, I built it using :


python insane.py -l DPPC -x 6 -y 6 -z 7.498 -pbc cubic -sol w -o 
dppc.gro
-p system.top


I do minimization and NPT equilibrium. but when I load it with 200bar or
even 100 bar the system fail less than 1ns but the article gain for 200
bar, a time period of 8ns� and for 100 bar, no pore formation. oddly
when I load it with 50bar I can elicit the correct answer for Area per
lipid for the example.( I obtain 0.74 which is ok based on the
article)


any comment on where probably I was wrong ? I really apreciate it.


best regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran

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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

Hi all,

Hoping this will be the final stumbling block. I’ve successfully minimised
my structure to a a very small max force:
Potential Energy  = -1.93736854460113e+03
Maximum force =  7.39399083846082e-04 on atom 34
Norm of force =  1.64068483698544e-04


When I perform integrator=nm there are no warning of potential imaginary
(negative) values. However, upon running:
g_nmeig_d -f dogdic_nma.mtx -s dogdic_nma.tpr -last 3000
I see the following:



Full matrix storage format, nrow=279, ncols=279
Diagonalizing to find vectors 1 through 279...

One of the lowest 6 eigenvalues has a non-zero value.

This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...

Back Off! I just backed up eigenval.xvg to ./#eigenval.xvg.2#
Writing eigenfrequencies - negative eigenvalues will be set to zero.




My lowest 6 eigenvalues are:
1   0.0780823
 20.153357
 30.174772
 40.327362
 50.466203
 6 0.64693


I’m a little confused by the statement "One of the lowest 6 eigenvalues
has a non-zero value. This could mean that the reference structure was not
properly energy minimized.” Really? Surely it out to be if one or more of
the values is negative.  Also, there were no eigenvalues set to zero
(hence, I can only assume I have no negative eigenvalues).

Would appreciate a little insight.
Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 16:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Nash, Anthony"
 wrote:

>Dear Mark and Justin,
>
>By removing the restraints (your suggestions) it appears to have worked!
>
>Maximum force: 9.21098e-04
>Writing Hessian...
>
>This now matches the same force as my energy minimisation. Many thanks for
>you help.
>
>Thanks
>Anthony
>
>
>
>Dr Anthony Nash
>Department of Chemistry
>University College London
>
>
>
>
>
>On 29/02/2016 14:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>behalf of Mark Abraham" on behalf of mark.j.abra...@gmail.com> wrote:
>
>>Hi,
>>
>>An earlier mdp file suggested you were using position restraints. There
>>should be no need for this, nor any problem, but what happens without
>>them?
>>
>>Mark
>>
>>On Mon, 29 Feb 2016 15:39 Nash, Anthony  wrote:
>>
>>> Hi Justin,
>>>
>>> After some digging I had found that link and made some adjustments (as
>>> presented in the later email).
>>>
>>> After a series of energy minimisations (including switching LINCS off,
>>>and
>>> dropping the energy step to a very small number), and with the final
>>> command:
>>> grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
>>> modic_cg_3.trr
>>>
>>>
>>> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883
>>>steps
>>> Potential Energy  = -1.92681826422996e+03
>>> Maximum force =  8.54361662283108e-04 on atom 44
>>> Norm of force =  2.71110116926712e-04
>>>
>>>
>>> However, when switching to integrator=nm, running grompp_d -f nma.mdp
>>>-c
>>> modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
>>> mdrun_d, I get:
>>>
>>> Maximum force: 5.19179e+01
>>> The force is probably not small enough to ensure that you are at a
>>>minimum.
>>> Be aware that negative eigenvalues may occur
>>> when the resulting matrix is diagonalized.
>>>
>>>
>>>
>>> I¹m still struggling to yield a maximum force during the integrator=nm
>>> step, as presented from the earlier cg step. The .mdp files are
>>>identical
>>> with the exception of the integrator line.
>>>
>>> Thanks
>>> Anthony
>>>
>>>
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>>
>>>
>>>
>>>
>>>
>>> On 29/02/2016 12:49, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>>on
>>> behalf of Justin Lemkul"
>>> >> jalem...@vt.edu> wrote:
>>>
>>> >
>>> >
>>> >On 2/29/16 3:41 AM, Nash, Anthony wrote:
>>> >> Hi Tsjerk,
>>> >>
>>> >> The two .mdp files are virtually identical (the only exception being
>>> >>what
>>> >> defines one as a conjugate-gradient, and the other for normal mode
>>> >> analysis):
>>> >>
>>> >> CONJUGATE GRADIENT:
>>> >> define = -DPOSRES
>>> >> integrator  = cg
>>> >> emtol   = 0.001
>>> >> emstep  = 0.0002
>>> >> nsteps  = 100
>>> >> nstcgsteep  = 100
>>> >> cutoff-scheme = verlet
>>> >> nstlist = 10
>>> >> ns_type = grid
>>> >> rlist   = 1.4
>>> >> coulombtype = PME
>>> >> rcoulomb= 1.4
>>> >> rvdw= 1.4
>>> >> pbc = xyz
>>> >>
>>> >>
>>> >> NORMAL MODE ANALYSIS
>>> >> define = -DPOSRES
>>> >> integrator = nm
>>> >> emtol = 0.001
>>> >> emstep = 0.0002
>>> >> nsteps = 100
>>> 

Re: [gmx-users] magnetic field

[Kowsar Khajeh]

Magnetic field and electric are not same.also, they have not same effect.
my molecule is asphaltene.
Thanks for your answer

On Monday, February 29, 2016, Kowsar Khajeh  wrote:
> Hello.
> My question is that;
> Does it possible to apply an external field ( like magnetic field ) to
the polar molecules in the simulation box in gromacs? in fact, can we
define polar molecules in the box?
> thanks
>
> Kosar Khajeh
> =
> PhD Candidate
>
> Faculty of Mechanical Engineering
> University of Tabriz, Tabriz, Iran
>
>

-- 

Kosar Khajeh
=
PhD Candidate
Faculty of Mechanical Engineering
University of Tabriz, Tabriz, Iran
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Re: [gmx-users] nrexcl

[Mark Abraham]

Hi,

I expect that there isn't a maximum. But IIRC grompp tells you what it is
doing with exclusions, and the output of gmx dump -s your.tpr is definitive.

Mark

On Mon, Feb 29, 2016 at 8:24 PM Parvez Mh  wrote:

> Dear all,
>
> I would like to know what is the maximum  *nrexcl* allowed in gromacs.
>
> Regards
> Masrul
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[gmx-users] nrexcl

[Parvez Mh]

Dear all,

I would like to know what is the maximum  *nrexcl* allowed in gromacs.

Regards
Masrul
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[gmx-users] Calculate energy associated with hydrogen bond

[Tushar Ranjan Moharana]

Hi Everyone,
Can anyone let me know how to calculate energy associated with hydrogen
bond? Particularly if I am not sure which one is the acceptor (or donor) or
there is a probability of more than one acceptor for a given donor or vice
versa.

Thanks a lot.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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[gmx-users] Box size for decoupled molecule in NpT ensemble

[Andreas Mecklenfeld]

Dear Gromacs-users,

I've a question regarding Gibbs free energy simulations. As the volume 
can fluctuate in the NpT-ensemble and is an extensive quantity, I do 
expect an intrinsic volume for the decoupled solute in the gas phase. Is 
there any chance to display this value?


Regards,
Andreas

--
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814

http://www.ift-bs.de

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Re: [gmx-users] generating martini-version of lipids

[Tsjerk Wassenaar]

Hi Jagannath,

Backward actually can do both. For conversion of a Gromos system use

backward.py -from gromos -to martini

Hope it helps,

Tsjerk


On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal  wrote:

> Dear Gromacs/Martini-users
>
> I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the
> Martini coarse-grained format. However, I found martinize.py script  does
> not transform lipid or waters to coarse-grained counterpart.It only works
> for protein. So, Is there any particular way I can generate the CG version
> of my atomistic DPPG/water bilayer ?
>
> I guess backward scripts does the reverse of what I am trying to achieve.
> So, if you can suggest a way to generate a coarse-grained pdb files of the
> atomistic lipid bilayer/water, that will be very helpful.
>
> Jagannath
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

Dear Mark and Justin,

By removing the restraints (your suggestions) it appears to have worked!

Maximum force: 9.21098e-04
Writing Hessian...

This now matches the same force as my energy minimisation. Many thanks for
you help.

Thanks
Anthony



Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 14:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>An earlier mdp file suggested you were using position restraints. There
>should be no need for this, nor any problem, but what happens without
>them?
>
>Mark
>
>On Mon, 29 Feb 2016 15:39 Nash, Anthony  wrote:
>
>> Hi Justin,
>>
>> After some digging I had found that link and made some adjustments (as
>> presented in the later email).
>>
>> After a series of energy minimisations (including switching LINCS off,
>>and
>> dropping the energy step to a very small number), and with the final
>> command:
>> grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
>> modic_cg_3.trr
>>
>>
>> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883
>>steps
>> Potential Energy  = -1.92681826422996e+03
>> Maximum force =  8.54361662283108e-04 on atom 44
>> Norm of force =  2.71110116926712e-04
>>
>>
>> However, when switching to integrator=nm, running grompp_d -f nma.mdp -c
>> modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
>> mdrun_d, I get:
>>
>> Maximum force: 5.19179e+01
>> The force is probably not small enough to ensure that you are at a
>>minimum.
>> Be aware that negative eigenvalues may occur
>> when the resulting matrix is diagonalized.
>>
>>
>>
>> I¹m still struggling to yield a maximum force during the integrator=nm
>> step, as presented from the earlier cg step. The .mdp files are
>>identical
>> with the exception of the integrator line.
>>
>> Thanks
>> Anthony
>>
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>>
>>
>> On 29/02/2016 12:49, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Justin Lemkul"
>> > jalem...@vt.edu> wrote:
>>
>> >
>> >
>> >On 2/29/16 3:41 AM, Nash, Anthony wrote:
>> >> Hi Tsjerk,
>> >>
>> >> The two .mdp files are virtually identical (the only exception being
>> >>what
>> >> defines one as a conjugate-gradient, and the other for normal mode
>> >> analysis):
>> >>
>> >> CONJUGATE GRADIENT:
>> >> define = -DPOSRES
>> >> integrator  = cg
>> >> emtol   = 0.001
>> >> emstep  = 0.0002
>> >> nsteps  = 100
>> >> nstcgsteep  = 100
>> >> cutoff-scheme = verlet
>> >> nstlist = 10
>> >> ns_type = grid
>> >> rlist   = 1.4
>> >> coulombtype = PME
>> >> rcoulomb= 1.4
>> >> rvdw= 1.4
>> >> pbc = xyz
>> >>
>> >>
>> >> NORMAL MODE ANALYSIS
>> >> define = -DPOSRES
>> >> integrator = nm
>> >> emtol = 0.001
>> >> emstep = 0.0002
>> >> nsteps = 100
>> >> cutoff-scheme = verlet
>> >> nstlist = 10
>> >> ns_type = grid
>> >> rlist = 1.4
>> >> coulombtype = PME
>> >> rcoulomb = 1.4
>> >> rvdw = 1.4
>> >> pbc = xyz
>> >>
>> >>
>> >> The cg energy minimisation did NOT result in any warning about force
>>not
>> >> converging. The result I got (I just re did it now) was:
>> >> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994
>> >>steps
>> >> Potential Energy  = -1.73087278108256e+03
>> >> Maximum force =  9.97199385029354e-04 on atom 72
>> >> Norm of force =  4.63373534634654e-04
>> >>
>> >>
>> >> But then when I run normal mode analysis (integrator=nm) I get:
>> >> Maximum force: 6.97334e+02
>> >> The force is probably not small enough to ensure that you are at a
>> >>minimum.
>> >> Be aware that negative eigenvalues may occur
>> >> when the resulting matrix is diagonalized.
>> >>
>> >>
>> >> My work flow:
>> >> grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
>> >> mdrun_d -deffnm modic_cg
>> >> grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
>> >> mdrun_d -deffnm modic_nma
>> >>
>> >
>> >Relying only on .gro format is insufficient precision to continue from
>> >minimization to NMA.  Make sure to pass the .trr to grompp -t.
>> >
>> >http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>> >
>> >-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
>> >

[gmx-users] Note of geometric combination rules in LJ-PME

[badamkhatan togoldor]

Dear GmxUsers,



Recently I got this Note in my enegy minimization (l-bfgs) step. I am using 
5.1.1 version. 
  You are using geometric combination rules in LJ-PME, but your non-bonded  C6 
parameters do not follow these rules. This will introduce very small  errors in 
the forces and energies in your simulations. Dispersion  correction will 
correct total energy and/or pressure for isotropic  systems, but not forces or 
surface tensions.
Here is my part of em_l-bfgs.mdp option. 
cutoff-scheme            = verletnstlist                  = 10ns-type           
       = gridpbc                      = xyzrlist                    = 1.2; 
Electrostaticscoulombtype              = PMErcoulomb                 = 1.2; van 
der Waalsvdwtype                  = pmervdw-switch              = 1.0rvdw       
              = 1.2; Apply long range dispersion corrections for Energy and 
PressureDispCorr                  = EnerPres; Spacing for the PME/PPPM FFT 
gridfourierspacing           = 0.12; EWALD/PME/PPPM parameterspme_order         
       = 4ewald_rtol               = 1e-05epsilon_surface          = 0; 
Temperature and pressure coupling are off during EMtcoupl                   = 
nopcoupl                   = no
Please, any suggestion to get rid of this Note! Thank you  Hatan 

  
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Mark Abraham]

Hi,

An earlier mdp file suggested you were using position restraints. There
should be no need for this, nor any problem, but what happens without them?

Mark

On Mon, 29 Feb 2016 15:39 Nash, Anthony  wrote:

> Hi Justin,
>
> After some digging I had found that link and made some adjustments (as
> presented in the later email).
>
> After a series of energy minimisations (including switching LINCS off, and
> dropping the energy step to a very small number), and with the final
> command:
> grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
> modic_cg_3.trr
>
>
> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883 steps
> Potential Energy  = -1.92681826422996e+03
> Maximum force =  8.54361662283108e-04 on atom 44
> Norm of force =  2.71110116926712e-04
>
>
> However, when switching to integrator=nm, running grompp_d -f nma.mdp -c
> modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
> mdrun_d, I get:
>
> Maximum force: 5.19179e+01
> The force is probably not small enough to ensure that you are at a minimum.
> Be aware that negative eigenvalues may occur
> when the resulting matrix is diagonalized.
>
>
>
> I¹m still struggling to yield a maximum force during the integrator=nm
> step, as presented from the earlier cg step. The .mdp files are identical
> with the exception of the integrator line.
>
> Thanks
> Anthony
>
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> On 29/02/2016 12:49, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Justin Lemkul"
>  jalem...@vt.edu> wrote:
>
> >
> >
> >On 2/29/16 3:41 AM, Nash, Anthony wrote:
> >> Hi Tsjerk,
> >>
> >> The two .mdp files are virtually identical (the only exception being
> >>what
> >> defines one as a conjugate-gradient, and the other for normal mode
> >> analysis):
> >>
> >> CONJUGATE GRADIENT:
> >> define = -DPOSRES
> >> integrator  = cg
> >> emtol   = 0.001
> >> emstep  = 0.0002
> >> nsteps  = 100
> >> nstcgsteep  = 100
> >> cutoff-scheme = verlet
> >> nstlist = 10
> >> ns_type = grid
> >> rlist   = 1.4
> >> coulombtype = PME
> >> rcoulomb= 1.4
> >> rvdw= 1.4
> >> pbc = xyz
> >>
> >>
> >> NORMAL MODE ANALYSIS
> >> define = -DPOSRES
> >> integrator = nm
> >> emtol = 0.001
> >> emstep = 0.0002
> >> nsteps = 100
> >> cutoff-scheme = verlet
> >> nstlist = 10
> >> ns_type = grid
> >> rlist = 1.4
> >> coulombtype = PME
> >> rcoulomb = 1.4
> >> rvdw = 1.4
> >> pbc = xyz
> >>
> >>
> >> The cg energy minimisation did NOT result in any warning about force not
> >> converging. The result I got (I just re did it now) was:
> >> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994
> >>steps
> >> Potential Energy  = -1.73087278108256e+03
> >> Maximum force =  9.97199385029354e-04 on atom 72
> >> Norm of force =  4.63373534634654e-04
> >>
> >>
> >> But then when I run normal mode analysis (integrator=nm) I get:
> >> Maximum force: 6.97334e+02
> >> The force is probably not small enough to ensure that you are at a
> >>minimum.
> >> Be aware that negative eigenvalues may occur
> >> when the resulting matrix is diagonalized.
> >>
> >>
> >> My work flow:
> >> grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
> >> mdrun_d -deffnm modic_cg
> >> grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
> >> mdrun_d -deffnm modic_nma
> >>
> >
> >Relying only on .gro format is insufficient precision to continue from
> >minimization to NMA.  Make sure to pass the .trr to grompp -t.
> >
> >http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
> >
> >-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!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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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] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

Hi Justin,

After some digging I had found that link and made some adjustments (as
presented in the later email).

After a series of energy minimisations (including switching LINCS off, and
dropping the energy step to a very small number), and with the final
command:
grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
modic_cg_3.trr


Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883 steps
Potential Energy  = -1.92681826422996e+03
Maximum force =  8.54361662283108e-04 on atom 44
Norm of force =  2.71110116926712e-04


However, when switching to integrator=nm, running grompp_d -f nma.mdp -c
modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
mdrun_d, I get:

Maximum force: 5.19179e+01
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.



I¹m still struggling to yield a maximum force during the integrator=nm
step, as presented from the earlier cg step. The .mdp files are identical
with the exception of the integrator line.

Thanks
Anthony 


Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 12:49, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
 wrote:

>
>
>On 2/29/16 3:41 AM, Nash, Anthony wrote:
>> Hi Tsjerk,
>>
>> The two .mdp files are virtually identical (the only exception being
>>what
>> defines one as a conjugate-gradient, and the other for normal mode
>> analysis):
>>
>> CONJUGATE GRADIENT:
>> define = -DPOSRES
>> integrator  = cg
>> emtol   = 0.001
>> emstep  = 0.0002
>> nsteps  = 100
>> nstcgsteep  = 100
>> cutoff-scheme = verlet
>> nstlist = 10
>> ns_type = grid
>> rlist   = 1.4
>> coulombtype = PME
>> rcoulomb= 1.4
>> rvdw= 1.4
>> pbc = xyz
>>
>>
>> NORMAL MODE ANALYSIS
>> define = -DPOSRES
>> integrator = nm
>> emtol = 0.001
>> emstep = 0.0002
>> nsteps = 100
>> cutoff-scheme = verlet
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.4
>> coulombtype = PME
>> rcoulomb = 1.4
>> rvdw = 1.4
>> pbc = xyz
>>
>>
>> The cg energy minimisation did NOT result in any warning about force not
>> converging. The result I got (I just re did it now) was:
>> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994
>>steps
>> Potential Energy  = -1.73087278108256e+03
>> Maximum force =  9.97199385029354e-04 on atom 72
>> Norm of force =  4.63373534634654e-04
>>
>>
>> But then when I run normal mode analysis (integrator=nm) I get:
>> Maximum force: 6.97334e+02
>> The force is probably not small enough to ensure that you are at a
>>minimum.
>> Be aware that negative eigenvalues may occur
>> when the resulting matrix is diagonalized.
>>
>>
>> My work flow:
>> grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
>> mdrun_d -deffnm modic_cg
>> grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
>> mdrun_d -deffnm modic_nma
>>
>
>Relying only on .gro format is insufficient precision to continue from
>minimization to NMA.  Make sure to pass the .trr to grompp -t.
>
>http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>
>-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!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] protein-DNA complex

[Justin Lemkul]

On 2/29/16 4:25 AM, Mahboobeh Eslami wrote:

dear Justin
thanks for your answer
I have another question. Which of the following items is better in mdp file for
the equilibration and MD production steps?

tc-grps   = Protein-DNASOL-ION

or
tc-grps   = Protein   DNA   SOL-ION



Probably irrelevant if the protein and DNA are of reasonably large size.  I 
would probably couple the complex together.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Acpype topolgy error

[Justin Lemkul]

On 2/29/16 4:51 AM, Abid Channa wrote:

Dear Gromacs users,
I am going to run complex simulation. I have prepared ligand topology through acpype , 
from where I have taken two files .gro and .itp file. I have used Gromos ff for my 
simulation . I got atom type error while running this command  " gmx grompp -f 
em.mdp -c solv.gro -p topol.top -o ions.tpr". My acpype taken .itp file is like [ 
atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
  1   ca 1   THAC11-0.119000 12.01000 ; qtot -0.119
  2   ca 1   THAC22-0.173300 12.01000 ; qtot -0.292
  3   ca 1   THAC33 0.430600 12.01000 ; qtot 0.138
  4   ca 1   THAC44-0.182300 12.01000 ; qtot -0.044
  5   ca 1   THAC55-0.105000 12.01000 ; qtot -0.149It 
gave following error
Fatal error:
Atomtype ca not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Kindly suggest me How can I resolve this problem.



There are probably new [atomtypes] in the topology that you haven't included. 
Atom types are case-sensitive and lowercase types are often used to avoid 
conflicts with the parent force field.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Justin Lemkul]

On 2/29/16 3:41 AM, Nash, Anthony wrote:

Hi Tsjerk,

The two .mdp files are virtually identical (the only exception being what
defines one as a conjugate-gradient, and the other for normal mode
analysis):

CONJUGATE GRADIENT:
define = -DPOSRES
integrator  = cg
emtol   = 0.001
emstep  = 0.0002
nsteps  = 100
nstcgsteep  = 100
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
rlist   = 1.4
coulombtype = PME
rcoulomb= 1.4
rvdw= 1.4
pbc = xyz


NORMAL MODE ANALYSIS
define = -DPOSRES
integrator = nm
emtol = 0.001
emstep = 0.0002
nsteps = 100
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
rlist = 1.4
coulombtype = PME
rcoulomb = 1.4
rvdw = 1.4
pbc = xyz


The cg energy minimisation did NOT result in any warning about force not
converging. The result I got (I just re did it now) was:
Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994 steps
Potential Energy  = -1.73087278108256e+03
Maximum force =  9.97199385029354e-04 on atom 72
Norm of force =  4.63373534634654e-04


But then when I run normal mode analysis (integrator=nm) I get:
Maximum force: 6.97334e+02
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.


My work flow:
grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
mdrun_d -deffnm modic_cg
grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
mdrun_d -deffnm modic_nma



Relying only on .gro format is insufficient precision to continue from 
minimization to NMA.  Make sure to pass the .trr to grompp -t.


http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

-Justin

--
==

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

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

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

==
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Re: [gmx-users] Coarse Grain using martinize.py

[Jagannath Mondal]

Dear Tsjerk
  I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an atomistic
simulation), how do I generate a coarse-grained martini counter-part of
that specific atomistic snapshot ?

Your suggestion will be very helpful.

On Sat, Feb 27, 2016 at 3:29 AM, Tsjerk Wassenaar  wrote:

> Hi Ali,
>
> The current version of martinize is for coarse graining proteins and
> there's a version for nucleic acids. Lipids are not supported yet. These
> you could forward map with the program backward, but why the hassle as you
> can also directly build the coarse grain membrane/solvent system with
> insane (http://www.cgmartini.nl/index.php/downloads/tools/239-insane).
>
> Hope it helps,
>
> Tsjerk
> On Feb 26, 2016 22:36,  wrote:
>
>
>
> Dear all
> I want to simulate a system of 128 DPPC with 3655 water molecule which its
> .pdb file is available on professor tielman website. I want to Coarse
> grain it but apparently at first i should turn the pdb file into
> appropriate type for using with martini. I understood, I should use marti
> ize.py to convert the pdb but I dont know how. Also the tutorial wasnt
> helpful. Could anyone give me the direct command to do this ?
> best regards
> Ali
> ==
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
> --
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Re: [gmx-users] Sulfate ion parameters

[Mark Abraham]

Hi,

Such questions are why all published articles list the email address of a
"corresponding author" ;-) But first, be sure their model wasn't designed
to be rigid, and so have no internal parameters such as you are seeking.

Mark

On Mon, Feb 29, 2016 at 12:01 PM #SUKRITI GUPTA# 
wrote:

> Thanks for the reply.
>
> I got one paper stating non bonded parameter values for sulphate ions:
> "Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic
> Properties", but this paper does not provide bonded parameters required for
> simulating sulfate ions, i.e. bond bending and stretching parameters. Is
> there a way to find what parameters were used in the study.
>
> Thanks and Regards
> Sukriti
>
>
>
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N)
> | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christian
> Bope Domilongo 
> Sent: Wednesday, February 24, 2016 4:43 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Sulfate ion parameters
>
> You may try to generate topology file using Topolbuilder
> http://www.gromacs.org/Downloads/User_contributions/Other_software
> Regards,
>
>
> On 24 February 2016 at 14:16, #SUKRITI GUPTA# 
> wrote:
>
> > Dear gromacs users,
> >
> >
> > I wanted to simulate sulphate ions in water using oplsaa force field but
> I
> > couldn't find parameters for sulphur and oxygen atoms of sulphate ions in
> > the oplsaa force field files. Can anyone suggest from where can I get
> these
> > parameters?
> >
> >
> > Charmm force field has the parameters for sulphate ions, so is it
> possible
> > to use those parameters itself for simulations? Also the partial charges
> > given in charmm force field to S and O of sulphate ions do not add up to
> > -2. (S +1.33, O -0.78) So how to select the correct partial charges here?
> >
> >
> > Thanks and Regards
> >
> > Sukriti
> >
> >
> > [
> >
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3
> > ]
> >
> > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N
> )
> > | Nanyang Technological University
> > N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> > Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:
> > erian.ntu.edu.sg
> >
> >
> >
> > --
> > Gromacs Users mailing list
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Bope Domilongo Christian
> Ph.D candidate in Computational Biology
> Division of Structural Biology and Biochemistry
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> +6590565804
> http://www.ntu.edu.sg/
> --
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[gmx-users] Fw: protein-DNA complex

[Mahboobeh Eslami]

 On Monday, February 29, 2016 12:55 PM, Mahboobeh Eslami 
 wrote:
 

 dear Justinthanks for your answerI have another question. Which of the 
following items is better in mdp file for the equilibration and MD production 
steps?
tc-grps   = Protein-DNASOL-ION
or tc-grps   = Protein   DNA   SOL-ION
Sincerely thank youbest 

On Saturday, February 27, 2016 3:46 PM, Justin Lemkul  
wrote:
 

 

On 2/27/16 3:03 AM, Mahboobeh Eslami wrote:
> hi all I want to do molecular dynamics simulations on protein-DNA complex.
> should  the simulation of  protein-DNA complex be done like the
> protein-protein complex? or is it  better to select different force field for
> protein and DNA separately in MD simulation of protein-DNA?  How is simulated
> protein-DNA complex? Thanks so much for your help.
>

It's just like simulating any other molecule-in-water system, be it a single or 
multiple proteins.  You shouldn't choose different force fields, because mixing 
and matching is generally a very (very very very) bad idea.  All modern 
biomolecular force fields support proteins, DNA, and more.  Read up on the 
quality of each before moving on; for instance, the AMBER implementations in 
GROMACS rely on very outdated AMBER nucleic acid force fields, and should be 
replaced with the more recent parameter sets. I believe some of these are 
available on the GROMACS user contributions page, but the validation issues, 
AFAIK, were never resolved, so check carefully...

-Justin

-- 
==

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

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

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

==


   

  
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Re: [gmx-users] magnetic field

[Mark Abraham]

Hi,

On Mon, Feb 29, 2016 at 10:56 AM Kowsar Khajeh 
wrote:

> Hello.
> My question is that;
> Does it possible to apply an external field ( like magnetic field ) to the
> polar molecules in the simulation box in gromacs?


Yes, there's a (very small) part in the reference manual about applying an
external electric field.

in fact, can we define
> polar molecules in the box?
>

Yes - but what do you mean?

Mark


> thanks
>
> Kosar Khajeh
> =
> PhD Candidate
> Faculty of Mechanical Engineering
> University of Tabriz, Tabriz, Iran
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Re: [gmx-users] Sulfate ion parameters

[#SUKRITI GUPTA#]

Thanks for the reply. 

I got one paper stating non bonded parameter values for sulphate ions: "Sulfate 
Anion in Water: Model Structural, Thermodynamic, and Dynamic Properties", but 
this paper does not provide bonded parameters required for simulating sulfate 
ions, i.e. bond bending and stretching parameters. Is there a way to find what 
parameters were used in the study.

Thanks and Regards
Sukriti




Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Christian Bope 
Domilongo 
Sent: Wednesday, February 24, 2016 4:43 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Sulfate ion parameters

You may try to generate topology file using Topolbuilder
http://www.gromacs.org/Downloads/User_contributions/Other_software
Regards,


On 24 February 2016 at 14:16, #SUKRITI GUPTA# 
wrote:

> Dear gromacs users,
>
>
> I wanted to simulate sulphate ions in water using oplsaa force field but I
> couldn't find parameters for sulphur and oxygen atoms of sulphate ions in
> the oplsaa force field files. Can anyone suggest from where can I get these
> parameters?
>
>
> Charmm force field has the parameters for sulphate ions, so is it possible
> to use those parameters itself for simulations? Also the partial charges
> given in charmm force field to S and O of sulphate ions do not add up to
> -2. (S +1.33, O -0.78) So how to select the correct partial charges here?
>
>
> Thanks and Regards
>
> Sukriti
>
>
> [
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3
> ]
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N)
> | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
>
>
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--
Bope Domilongo Christian
Ph.D candidate in Computational Biology
Division of Structural Biology and Biochemistry
School of Biological Sciences
Nanyang Technological University
Singapore
+6590565804
http://www.ntu.edu.sg/
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Re: [gmx-users] Coarse Grain using martinize.py

[jagannath mondal]

Dear Tsjerk
  I had a similar question. I guess insane.py script is supposed to build a
coarse-grained membrane/solvent system from scratch. But, if I already have
a particular existing atomistic configuration of lipid/water system along
with some proteins ( which I had obtained by performing an atomistic
simulation), how do I generate a coarse-grained martini counter-part of
that specific atomistic snapshot ?

Your suggestion will be very helpful.

jagannath


On Sat, Feb 27, 2016 at 3:29 AM, Tsjerk Wassenaar  wrote:

> Hi Ali,
>
> The current version of martinize is for coarse graining proteins and
> there's a version for nucleic acids. Lipids are not supported yet. These
> you could forward map with the program backward, but why the hassle as you
> can also directly build the coarse grain membrane/solvent system with
> insane (http://www.cgmartini.nl/index.php/downloads/tools/239-insane).
>
> Hope it helps,
>
> Tsjerk
> On Feb 26, 2016 22:36,  wrote:
>
>
>
> Dear all
> I want to simulate a system of 128 DPPC with 3655 water molecule which its
> .pdb file is available on professor tielman website. I want to Coarse
> grain it but apparently at first i should turn the pdb file into
> appropriate type for using with martini. I understood, I should use marti
> ize.py to convert the pdb but I dont know how. Also the tutorial wasnt
> helpful. Could anyone give me the direct command to do this ?
> best regards
> Ali
> ==
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
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[gmx-users] generating martini-version of lipids

[Jagannath Mondal]

Dear Gromacs/Martini-users

I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the
Martini coarse-grained format. However, I found martinize.py script  does
not transform lipid or waters to coarse-grained counterpart.It only works
for protein. So, Is there any particular way I can generate the CG version
of my atomistic DPPG/water bilayer ?

I guess backward scripts does the reverse of what I am trying to achieve.
So, if you can suggest a way to generate a coarse-grained pdb files of the
atomistic lipid bilayer/water, that will be very helpful.

Jagannath
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

I noticed that I hadn’t included LINCS parameters in the mdp file. I have
included and currently running using:

continuation = no
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 2 ; accuracy of LINCS
lincs_order = 8 ; also related to accuracy


I upped lincs_iter from 1 to 2, and lincs_order from 4 to 8. The manual
says this is ideal for increasing accuracy during energy minimisation.

After performing this run I’m now getting forces beyond Fmax and I’ve
reached the maximum number of steps.
Potential Energy  = -1.71320900832000e+03
Maximum force =  1.80888456004520e+01 on atom 13
Norm of force =  7.70125465905422e+00


Prior to including LINCS, the system was finishing within 1000 steps, so I
feel as though I’m heading down the right paths in trying to get these
forces down first now that I’ve included lincs.




Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 08:41, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Nash, Anthony"
 wrote:

>Hi Tsjerk,
>
>The two .mdp files are virtually identical (the only exception being what
>defines one as a conjugate-gradient, and the other for normal mode
>analysis):
>
>CONJUGATE GRADIENT:
>define = -DPOSRES
>integrator  = cg
>emtol   = 0.001
>emstep  = 0.0002
>nsteps  = 100
>nstcgsteep  = 100
>cutoff-scheme = verlet
>nstlist = 10
>ns_type = grid
>rlist   = 1.4
>coulombtype = PME
>rcoulomb= 1.4
>rvdw= 1.4
>pbc = xyz
>
>
>NORMAL MODE ANALYSIS
>define = -DPOSRES
>integrator = nm 
>emtol = 0.001 
>emstep = 0.0002 
>nsteps = 100 
>cutoff-scheme = verlet
>nstlist = 10
>ns_type = grid 
>rlist = 1.4 
>coulombtype = PME 
>rcoulomb = 1.4 
>rvdw = 1.4 
>pbc = xyz 
>
>
>The cg energy minimisation did NOT result in any warning about force not
>converging. The result I got (I just re did it now) was:
>Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994 steps
>Potential Energy  = -1.73087278108256e+03
>Maximum force =  9.97199385029354e-04 on atom 72
>Norm of force =  4.63373534634654e-04
>
>
>But then when I run normal mode analysis (integrator=nm) I get:
>Maximum force: 6.97334e+02
>The force is probably not small enough to ensure that you are at a
>minimum.
>Be aware that negative eigenvalues may occur
>when the resulting matrix is diagonalized.
>
>
>My work flow:
>grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
>mdrun_d -deffnm modic_cg
>grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
>mdrun_d -deffnm modic_nma
>
>
>
>
>
>
>I sincerely hope I’m doing something wrong. That way it’ll be easier to
>solve. 
>
>Many thanks
>Anthony
>
>
>Dr Anthony Nash
>Department of Chemistry
>University College London
>
>
>
>
>
>On 29/02/2016 08:03, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>behalf of Tsjerk Wassenaar"
>tsje...@gmail.com> wrote:
>
>>Hi Anthony,
>>
>>You can paste your exact workflow commands and mdp files, but that would
>>be
>>to just check whether you overlooked something. If you assert that the
>>mdp
>>files are the same, except for the integrator and you really did use the
>>final minimized structure as input for the nm run, then it seems
>>something's fishy. You could make a run input file with integrator=cg and
>>integrator=nm and compare the two tpr files to see if something was
>>changed
>>implicitly.
>>
>>Cheers,
>>
>>Tsjerk
>>
>>On Mon, Feb 29, 2016 at 6:57 AM, Nash, Anthony  wrote:
>>
>>> Hi Tsjerk,
>>>
>>> Compiled in double precision. I’ve alternated between steepest and
>>> conjugate gradient. I am slightly confused over why the energy
>>> minimisation reports a "Maximum force =  3.72351263315387e-05 on
>>>atom
>>> 34” only then for integrator=nm to report "Maximum force: 6.02183e+02”,
>>> which will presumably return in an imaginary frequency (I haven’t tried
>>>-
>>> yet even if it didn’t I would be suspicious given the earlier warning).
>>>
>>> Thanks
>>> Anthony
>>>
>>>
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>>
>>>
>>>
>>>
>>>
>>> On 28/02/2016 22:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>>on
>>> behalf of Tsjerk Wassenaar"
>>> >> tsje...@gmail.com> wrote:
>>>
>>> >Hi Anthony,
>>> >
>>> >You do not state whether Gromacs was compiled in double precision or
>>>not.
>>> >It should be for this stuff. In addition, you can try another
>>>minimization
>>> >method. Sometimes alternating minimization methods may help to reach a
>>> >proper minimum.
>>> >
>>> >Cheers,
>>> >
>>> >Tsjerk
>>> >
>>> >On Sun, Feb 28, 2016 at 11:27 AM, Nash, Anthony 

[gmx-users] magnetic field

[Kowsar Khajeh]

Hello.
My question is that;
Does it possible to apply an external field ( like magnetic field ) to the
polar molecules in the simulation box in gromacs? in fact, can we define
polar molecules in the box?
thanks

Kosar Khajeh
=
PhD Candidate
Faculty of Mechanical Engineering
University of Tabriz, Tabriz, Iran
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[gmx-users] Acpype topolgy error

[Abid Channa]

Dear Gromacs users,
I am going to run complex simulation. I have prepared ligand topology through 
acpype , from where I have taken two files .gro and .itp file. I have used 
Gromos ff for my simulation . I got atom type error while running this command  
" gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr". My acpype taken 
.itp file is like [ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
 1   ca 1   THA    C1    1    -0.119000 12.01000 ; qtot -0.119
 2   ca 1   THA    C2    2    -0.173300 12.01000 ; qtot -0.292
 3   ca 1   THA    C3    3 0.430600 12.01000 ; qtot 0.138
 4   ca 1   THA    C4    4    -0.182300 12.01000 ; qtot -0.044
 5   ca 1   THA    C5    5    -0.105000 12.01000 ; qtot -0.149It 
gave following error
Fatal error:
Atomtype ca not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Kindly suggest me How can I resolve this problem.

Thanks
Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
 Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
 International Center for Chemical and Biological Sciences  (ICCBS),
 University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. 
(309)
 Cell # +923013553051.
http://www.iccs.edu/
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

Hi Tsjerk,

The two .mdp files are virtually identical (the only exception being what
defines one as a conjugate-gradient, and the other for normal mode
analysis):

CONJUGATE GRADIENT:
define = -DPOSRES
integrator  = cg
emtol   = 0.001
emstep  = 0.0002
nsteps  = 100
nstcgsteep  = 100
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
rlist   = 1.4
coulombtype = PME
rcoulomb= 1.4
rvdw= 1.4
pbc = xyz


NORMAL MODE ANALYSIS
define = -DPOSRES
integrator = nm 
emtol = 0.001 
emstep = 0.0002 
nsteps = 100 
cutoff-scheme = verlet
nstlist = 10
ns_type = grid 
rlist = 1.4 
coulombtype = PME 
rcoulomb = 1.4 
rvdw = 1.4 
pbc = xyz 


The cg energy minimisation did NOT result in any warning about force not
converging. The result I got (I just re did it now) was:
Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994 steps
Potential Energy  = -1.73087278108256e+03
Maximum force =  9.97199385029354e-04 on atom 72
Norm of force =  4.63373534634654e-04


But then when I run normal mode analysis (integrator=nm) I get:
Maximum force: 6.97334e+02
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.


My work flow:
grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
mdrun_d -deffnm modic_cg
grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
mdrun_d -deffnm modic_nma






I sincerely hope I’m doing something wrong. That way it’ll be easier to
solve. 

Many thanks
Anthony


Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 08:03, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Tsjerk Wassenaar"
 wrote:

>Hi Anthony,
>
>You can paste your exact workflow commands and mdp files, but that would
>be
>to just check whether you overlooked something. If you assert that the mdp
>files are the same, except for the integrator and you really did use the
>final minimized structure as input for the nm run, then it seems
>something's fishy. You could make a run input file with integrator=cg and
>integrator=nm and compare the two tpr files to see if something was
>changed
>implicitly.
>
>Cheers,
>
>Tsjerk
>
>On Mon, Feb 29, 2016 at 6:57 AM, Nash, Anthony  wrote:
>
>> Hi Tsjerk,
>>
>> Compiled in double precision. I’ve alternated between steepest and
>> conjugate gradient. I am slightly confused over why the energy
>> minimisation reports a "Maximum force =  3.72351263315387e-05 on
>>atom
>> 34” only then for integrator=nm to report "Maximum force: 6.02183e+02”,
>> which will presumably return in an imaginary frequency (I haven’t tried
>>-
>> yet even if it didn’t I would be suspicious given the earlier warning).
>>
>> Thanks
>> Anthony
>>
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>>
>>
>> On 28/02/2016 22:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Tsjerk Wassenaar"
>> > tsje...@gmail.com> wrote:
>>
>> >Hi Anthony,
>> >
>> >You do not state whether Gromacs was compiled in double precision or
>>not.
>> >It should be for this stuff. In addition, you can try another
>>minimization
>> >method. Sometimes alternating minimization methods may help to reach a
>> >proper minimum.
>> >
>> >Cheers,
>> >
>> >Tsjerk
>> >
>> >On Sun, Feb 28, 2016 at 11:27 AM, Nash, Anthony 
>>wrote:
>> >
>> >> Hi all,
>> >>
>> >> I would like to pull out the vibrational normal modes using gromacs
>> >>over a
>> >> customised fragment to compare back with the original QM frequency
>> >> analysis.
>> >>
>> >> I¹ve performed an integrator=cg over my structure, and monitored the
>> >> potential energy which converges. The forces also converge beneath
>>the
>> >> requested precision (as 0.0001, as per gromacs manual). The message:
>> >>
>> >> 
>> >>
>> >> Polak-Ribiere Conjugate Gradients:
>> >>Tolerance (Fmax)   =  1.0e-04
>> >>Number of steps=  100
>> >>F-max =  7.35939e+03 on atom 79
>> >>F-Norm=  1.68505e+03
>> >>
>> >> writing lowest energy coordinates.
>> >>
>> >> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 8350
>> >>steps
>> >> Potential Energy  = -1.67001242395943e+03
>> >> Maximum force =  3.72351263315387e-05 on atom 34
>> >> Norm of force =  1.20696019277311e-05
>> >>
>> >>
>> >> 
>> >>
>> >>
>> >> When I then come to run integrator=nm I get a maximum force at odds
>>with
>> >> the maximum force reported at the final stage of my energy
>>minimisation:
>> >>
>> >> 
>> >>
>> >> Maximum force: 6.02183e+02
>> >> The force is probably not small enough to ensure 

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

[Mark Abraham]

Hi,

The simplest explanation for this is that one set of runs used position
restraints and one set did not.

Mark

On Mon, 29 Feb 2016 08:48 SAPNA BORAH  wrote:

> hi
> Thanks for the suggestion. I will give this a shot, and remove these
> restraints.
>
> I am unclear about what should I be looking in the log file as you
> mentioned. The conformations are not just close, they are the same as the
> initial conformation.
>
> I have some understanding on pbc that serves a problem in visualisation of
> the trajectory. I have applied the all sorts of pbc options, but somehow
> things are not falling into place.
>
> However the problem more grave here, for me, is the production run and the
> model stability that is happening throughout the simulations in different
> versions.
>
>
> Thanks.
> Sapna
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
>
> On Mon, Feb 29, 2016 at 11:59 AM, Dries Van Rompaey <
> dries.vanromp...@gmail.com> wrote:
>
> > Hi,
> > Looks like you might be applying positional restraints (define =-DPOSRES
> in
> > your mdp file). This is standard practice for equilibration, but I don't
> > think you want to be doing this for your production run, as this will
> > restrain your protein to conformations rather close to your starting
> > conformation. Check if this is the case in your logfile.
> >
> > Proteins coming 'out of the box' is caused by periodic boundary
> conditions.
> > This is probably not a problem. Read this for more information:
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > Sometimes one pass of trjconv isn't enough to sort everything out and
> more
> > might be needed.
> >
> > Kind regards
> >
> > Dries
> > On 29 Feb 2016 5:25 a.m., "SAPNA BORAH"  wrote:
> >
> > > Dear Mark,
> > >
> > > I have still not been able to solve my problem. A whole new problem has
> > now
> > > arisen. I am listing them as follows:
> > >
> > > 1. I am running 100ns simulations for 6 protein models and I was using
> > both
> > > version 4.6.5 and 5.0.4 when I found that after production run, my
> > protein
> > > models are behaving differently in both the versions. I am attaching
> the
> > > images of rmsd differences in the link attached. Also, find the mdp
> files
> > > attached used in both the versions.
> > >
> > > 2. I have run multiple runs for the models to see if there are changes,
> > but
> > > everytime, each of the models is very very stable and does not change
> in
> > > conformation at all in 5.0.4 but does otherwise in 4.6.5.
> > >
> > > 3. There is another problem that the protein comes out of the water box
> > in
> > > 4.6.5 and not in 5.0.4 in all the simulations. I have ensured to remove
> > > jumps from the trajectories, make molecules whole.
> > >
> > > Please help me in this regard.
> > >
> > > http://dropcanvas.com/v0k0b
> > >
> > > Regards,
> > > Sapna.
> > >
> > > Sapna Mayuri Borah
> > > c/o Dr. A. N. Jha
> > > Research student
> > > Tezpur University,
> > > India
> > >
> > > On Thu, Feb 11, 2016 at 10:54 AM, Tsjerk Wassenaar 
> > > wrote:
> > >
> > > > Hi Sapna,
> > > >
> > > > The list doesn't allow attachments. Please put them somewhere online
> > and
> > > > provide a link.
> > > > The differences can be large. Can't tell if you don't know the
> possible
> > > > range of conformations/trajectories for one Gromacs version.
> > > > Did you ensure to remove jumps from the trajectories and/or make
> > > molecules
> > > > whole, etc? That would be the only thing we'd be able to see from the
> > > RMSD
> > > > plot anyway, whether you removed jumps or not. Otherwise it does not
> > > > contain useful information (in this regard).
> > > >
> > > > Cheers,
> > > >
> > > > Tsjerk
> > > > On Feb 11, 2016 05:28, "SAPNA BORAH"  wrote:
> > > >
> > > > > Dear Mark,
> > > > >
> > > > > Please find attached a plot showing the RMSD difference. It is for
> > the
> > > > same
> > > > > protein.
> > > > >
> > > > > Even if the same runs are not reproducible, my doubt is whether
> there
> > > can
> > > > > be such a large variation in the RMSD trend. Which data should I
> rely
> > > on
> > > > > then, it is giving me a hard time.
> > > > >
> > > > > I'll be grateful if you look into this.
> > > > >
> > > > > Thanks,
> > > > > Sapna.
> > > > >
> > > > > Sapna Mayuri Borah
> > > > > c/o Dr. A. N. Jha
> > > > > Research student
> > > > > Tezpur University,
> > > > > India
> > > > >
> > > > > On Tue, Feb 9, 2016 at 1:07 PM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > This is quite normal.
> > > > > > http://www.gromacs.org/Documentation/Terminology/Reproducibility
> .
> > > You
> > > > > > should see a similar range of variation in the trajectories
> > produced
> > > in
> > > > > the
> > > > > > two versions that are incompletely sampling the same 

[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

[Dries Van Rompaey]

On 29 February 2016 at 08:48, SAPNA BORAH  wrote:

> hi
> Thanks for the suggestion. I will give this a shot, and remove these
> restraints.
>
> I am unclear about what should I be looking in the log file as you
> mentioned. The conformations are not just close, they are the same as the
> initial conformation.
>
See if you can find "Position rest." in your logfile in the Energies
subsection.


>
> I have some understanding on pbc that serves a problem in visualisation of
> the trajectory. I have applied the all sorts of pbc options, but somehow
> things are not falling into place.


If you could post a screenshot of what it looks like that would be handy.
Currently there's not much else I can tell you.


>
>
However the problem more grave here, for me, is the production run and the
> model stability that is happening throughout the simulations in different
> versions.
>
> The model stability is probably caused by the postion restraints. If
you're telling gromacs to apply a restraint that penalizes movement of your
atoms, it makes sense that you won't be seeing much movement.
-- 
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Re: [gmx-users] Minimising forces for vibrational normal mode analysis

[Tsjerk Wassenaar]

Hi Anthony,

You can paste your exact workflow commands and mdp files, but that would be
to just check whether you overlooked something. If you assert that the mdp
files are the same, except for the integrator and you really did use the
final minimized structure as input for the nm run, then it seems
something's fishy. You could make a run input file with integrator=cg and
integrator=nm and compare the two tpr files to see if something was changed
implicitly.

Cheers,

Tsjerk

On Mon, Feb 29, 2016 at 6:57 AM, Nash, Anthony  wrote:

> Hi Tsjerk,
>
> Compiled in double precision. I’ve alternated between steepest and
> conjugate gradient. I am slightly confused over why the energy
> minimisation reports a "Maximum force =  3.72351263315387e-05 on atom
> 34” only then for integrator=nm to report "Maximum force: 6.02183e+02”,
> which will presumably return in an imaginary frequency (I haven’t tried -
> yet even if it didn’t I would be suspicious given the earlier warning).
>
> Thanks
> Anthony
>
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> On 28/02/2016 22:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Tsjerk Wassenaar"
>  tsje...@gmail.com> wrote:
>
> >Hi Anthony,
> >
> >You do not state whether Gromacs was compiled in double precision or not.
> >It should be for this stuff. In addition, you can try another minimization
> >method. Sometimes alternating minimization methods may help to reach a
> >proper minimum.
> >
> >Cheers,
> >
> >Tsjerk
> >
> >On Sun, Feb 28, 2016 at 11:27 AM, Nash, Anthony  wrote:
> >
> >> Hi all,
> >>
> >> I would like to pull out the vibrational normal modes using gromacs
> >>over a
> >> customised fragment to compare back with the original QM frequency
> >> analysis.
> >>
> >> I¹ve performed an integrator=cg over my structure, and monitored the
> >> potential energy which converges. The forces also converge beneath the
> >> requested precision (as 0.0001, as per gromacs manual). The message:
> >>
> >> 
> >>
> >> Polak-Ribiere Conjugate Gradients:
> >>Tolerance (Fmax)   =  1.0e-04
> >>Number of steps=  100
> >>F-max =  7.35939e+03 on atom 79
> >>F-Norm=  1.68505e+03
> >>
> >> writing lowest energy coordinates.
> >>
> >> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 8350
> >>steps
> >> Potential Energy  = -1.67001242395943e+03
> >> Maximum force =  3.72351263315387e-05 on atom 34
> >> Norm of force =  1.20696019277311e-05
> >>
> >>
> >> 
> >>
> >>
> >> When I then come to run integrator=nm I get a maximum force at odds with
> >> the maximum force reported at the final stage of my energy minimisation:
> >>
> >> 
> >>
> >> Maximum force: 6.02183e+02
> >> The force is probably not small enough to ensure that you are at a
> >>minimum.
> >> Be aware that negative eigenvalues may occur
> >> when the resulting matrix is diagonalized.
> >>
> >> 
> >>
> >>
> >>
> >> When I decrease the force tolerance in the integrator=cg energy
> >> minimisation to 0.1 I end up with a poorer force convergence
> >>(although
> >> the potential energy is almost the same, but also the integrator=nm will
> >> result in the same measure of maximum force):
> >>
> >> 
> >>
> >> Polak-Ribiere Conjugate Gradients:
> >>Tolerance (Fmax)   =  1.0e-05
> >>Number of steps=  100
> >>F-max =  7.35939e+03 on atom 79
> >>F-Norm=  1.68505e+03
> >>
> >> Energy minimization has stopped, but the forces have not converged to
> >>the
> >> requested precision Fmax < 1e-05 (which may not be possible for your
> >> system).
> >> It stopped because the algorithm tried to make a new step whose size was
> >> too
> >> small, or there was no change in the energy since last step. Either
> >>way, we
> >> regard the minimization as converged to within the available machine
> >> precision, given your starting configuration and EM parameters.
> >>
> >> writing lowest energy coordinates.
> >>
> >> Polak-Ribiere Conjugate Gradients converged to machine precision in 9839
> >> steps,
> >> but did not reach the requested Fmax < 1e-05.
> >> Potential Energy  = -1.67001242392665e+03
> >> Maximum force =  1.63690887039393e-03 on atom 34
> >> Norm of force =  3.34598700357485e-04
> >> 
> >>
> >>
> >>
> >> I don¹t want to end up with any imaginary values when I diagonalise the
> >> hessian, any idea how to improve this performance? I am concerned with
> >>the
> >> output "Energy minimization has stopped, but the forces have not
> >>converged
> >> to the requested precision Fmax < 1e-05 (which may not be possible for
> >> your system).² a a possible indication to the computational limitation
> >>of
> >> my