[gmx-users] Umbrella sampling - chain A does not get pulled

[Davide Mercadante]

Dear Justin,

I have been practicing umbrella sampling simulations following your tutorial
step by step. I have just finished to perform the pull simulations to
identify the configurations to use in the umbrella runs. I have used the
distances.pl script to run iteratively g_dist and the resulting file
(summary_distances.dat) is showing a distance between 2.62nm (for conf0.gro)
and 5.3nm (for conf500.gro). I don't seem to have the values reported in the
tutorial at all (in the tutorial is reported that the COM distance would be
something of an order of magnitude lowerŠ) and I am not sure if something is
gone wrong. 

I have also tried to visualize the trajectories but I am not able to see
chain_A moving away from the rest of the fibril. I have set, at the end of
the topol_Protein_chain_B.itp file, the lines suggested to restrain chain B.

#ifdef POSRES_B
#include "posre_Protein_chain_B.itp"
#endif

I have used all the input files given in the tutorial and the commands/files
extensions suggested.

Can you please help me to understand if I am doing something wrong?

Thank you very much for your help.
Davide





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[gmx-users] Is vacuum simulation NVT?

[Jong Wha Lee]

Dear Gromacs users,

 

Is a vacuum md simulation an NVT simulaton? As the pressure and energy are
not fixed, I think that the only option left is NVT. But without pbc, the
volume would not have been defined. Can it still be called NVT?

 

Thanks,

 

Jong Wha

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Re: [gmx-users] Error with MARTINI depending by the box size

[Tsjerk Wassenaar]

Hi,

Visualization is the key. If you check the structure right after genbox,
you should be able to notice something odd. Apparently genbox has a problem
with martini water, which probably means there is a problem with monoatomic
solvents. The problem has been noted before, b ut I'm a bit too lazy now to
check whether it was here or on the martini forum. Using a small box with a
single water molecule for filling will solve the problem.

Cheers,

Tsjerk


On Tue, Dec 11, 2012 at 12:06 AM, Mark Abraham wrote:

> On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/10/12 5:45 PM, francesco oteri wrote:
> >
> >> For Justin,
> >> I need this water for one simple reason: less then 20nm doesn't
> workAs
> >> I said before
> >>
> >>
> > It seems you have identified the source of the problem, and it is
> > independent of box size.  I questioned the box size because it seemed
> > rather random and you had not shown any data for box sizes less than 19
> nm,
> > so I was curious how you arrived at the need for 20 nm, more than double
> > the size of your solute.
> >
> > It would be interesting to see if you could identify a minimum box size
> > that does not require large numbers of solvent configurations to be
> stacked
> > within the unit cell.  The only reason I could see for what you're
> > reporting is if neighboring solvent blocks somehow get crossed to produce
> > overlap when they should simply be next to one another.  The larger the
> > box, the greater the probability that this happens.
>
>
> Yeah, that's probably it. The water box has many waters with x coordinates
> down at 0.000 and near 10.901, with an x size of 10.902. So different box
> sizes will randomly introduce unstable water configurations according to
> whether stuff is too close. This water box is probably not suited to the
> purpose - its "box size" might not include the half VDW radii outside the
> water coordinates needed to pack stably.
>
> Mark
>
>
> >
> >
> >> 2012/12/10 francesco oteri 
> >>
> >>  Hi Mark,
> >>> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest
> to
> >>> use 0.21. Since I still got errors with this procedure, I decided to
> >>> remove
> >>> water manually through vmd.
> >>>
> >>> Looking carefully at the configurations, I found that the water
> molecule
> >>> originating the error is exactly superimposed to an other molecule so I
> >>> simply deleted it and the same error is reported for an other water
> >>> molecule.
> >>>
> >>> Although I could scan all the pdb to detect all the superimposed water
> >>> molecules, I believed genbox checked for this. Of course the original
> box
> >>> does't contain superimposed molecules.
> >>>
> >>>
> >>>
> > It is highly unusual for genbox to produce overlapping waters, but per
> the
> > help description, only solute-solvent overlaps are checked, not
> > solvent-solvent, which would likely require enormous amounts of memory
> (and
> > genbox already has memory issues).
> >
> > -Justin
> >
> > --
> > ==**==
> >
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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Re: [gmx-users] gen-vel=no

[Venkat Reddy]

The check point file you submit will have the velocity information.


On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan
wrote:

> hi gmx user
>
> I've done a production simulation with gen_vel= no, but in grompp I forgot
> that use .trr file of equlibration simulation for initial velocities,
> my question is how gromacs treats with initial velocities  in this case?
>
> thanks in advance.
> --
> gmx-users mailing listgmx-users@gromacs.org
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] gen-vel=no

[Bahar Mehrpuyan]

hi gmx user

I've done a production simulation with gen_vel= no, but in grompp I forgot that 
use .trr file of equlibration simulation for initial velocities, 
my question is how gromacs treats with initial velocities  in this case?

thanks in advance.
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Re: [gmx-users] Error with MARTINI depending by the box size

[Mark Abraham]

On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul  wrote:

>
>
> On 12/10/12 5:45 PM, francesco oteri wrote:
>
>> For Justin,
>> I need this water for one simple reason: less then 20nm doesn't workAs
>> I said before
>>
>>
> It seems you have identified the source of the problem, and it is
> independent of box size.  I questioned the box size because it seemed
> rather random and you had not shown any data for box sizes less than 19 nm,
> so I was curious how you arrived at the need for 20 nm, more than double
> the size of your solute.
>
> It would be interesting to see if you could identify a minimum box size
> that does not require large numbers of solvent configurations to be stacked
> within the unit cell.  The only reason I could see for what you're
> reporting is if neighboring solvent blocks somehow get crossed to produce
> overlap when they should simply be next to one another.  The larger the
> box, the greater the probability that this happens.


Yeah, that's probably it. The water box has many waters with x coordinates
down at 0.000 and near 10.901, with an x size of 10.902. So different box
sizes will randomly introduce unstable water configurations according to
whether stuff is too close. This water box is probably not suited to the
purpose - its "box size" might not include the half VDW radii outside the
water coordinates needed to pack stably.

Mark


>
>
>> 2012/12/10 francesco oteri 
>>
>>  Hi Mark,
>>> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
>>> use 0.21. Since I still got errors with this procedure, I decided to
>>> remove
>>> water manually through vmd.
>>>
>>> Looking carefully at the configurations, I found that the water molecule
>>> originating the error is exactly superimposed to an other molecule so I
>>> simply deleted it and the same error is reported for an other water
>>> molecule.
>>>
>>> Although I could scan all the pdb to detect all the superimposed water
>>> molecules, I believed genbox checked for this. Of course the original box
>>> does't contain superimposed molecules.
>>>
>>>
>>>
> It is highly unusual for genbox to produce overlapping waters, but per the
> help description, only solute-solvent overlaps are checked, not
> solvent-solvent, which would likely require enormous amounts of memory (and
> genbox already has memory issues).
>
> -Justin
>
> --
> ==**==
>
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] Error with MARTINI depending by the box size

[Mark Abraham]

On Mon, Dec 10, 2012 at 11:44 PM, francesco oteri  wrote:

> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
> water manually through vmd.
>

Don't change things until you know *why* they don't work. That means
visualizing the results of the recommended workflow until you see a problem
emerge (which I think is in your starting protein configuration, if the
standard procedure also gave problems).

Why did you decide to double the margin to 0.8nm? You would create an
unphysical void, so numerical instability seems pretty likely. (But I think
you have a more serious problem as well.)

Even if this change was needed, you may as well do both clash-avoidance
procedures, in case there are things going on that you haven't thought of.

Looking carefully at the configurations, I found that the water molecule
> originating the error is exactly superimposed to an other molecule so I
> simply deleted it and the same error is reported for an other water
> molecule.
>
> Although I could scan all the pdb to detect all the superimposed water
> molecules, I believed genbox checked for this. Of course the original box
> does't contain superimposed molecules.
>

Shrug. You need to look at your intermediate structure files and find where
the problem first appears.

Mark


>
>
> Francesco
>
>
> 2012/12/10 Justin Lemkul 
>
> >
> >
> > On 12/10/12 5:15 PM, francesco oteri wrote:
> >
> >> Actually, since I copied and pasted the mail, there is an imprecision.
> >> When
> >> I use 20nm as box side lenght I don't get
> >> any error, everything goes fine.
> >>
> >> I actually tested different size between 19 and 20 nm and I found that
> the
> >> minimum size to avoid the error is 19.5nm.
> >> My system has an average size and, as stated by vmd, it size are
> >> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
> >> So a box of 20nm, as well as 19nm, is large enough to accomodate the
> >> protein.
> >>
> >>
> > Those box sizes are vast overkill.  Any reason why you need so much extra
> > water?
> >
> >
> >  Moreover, since I remove the water around the protein (that is already
> >> stabie because of the in vacuo minimization), the problem has to be in
> the
> >> bulk water!
> >>
> >>
> > As I said before, you should be able to identify the source of the
> problem
> > by simple visualization based on what mdrun has told you.
> >
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> > --
> > 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>
> >
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> --
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Re: [gmx-users] Error with MARTINI depending by the box size

[Justin Lemkul]

On 12/10/12 5:45 PM, francesco oteri wrote:

For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before



It seems you have identified the source of the problem, and it is independent of 
box size.  I questioned the box size because it seemed rather random and you had 
not shown any data for box sizes less than 19 nm, so I was curious how you 
arrived at the need for 20 nm, more than double the size of your solute.


It would be interesting to see if you could identify a minimum box size that 
does not require large numbers of solvent configurations to be stacked within 
the unit cell.  The only reason I could see for what you're reporting is if 
neighboring solvent blocks somehow get crossed to produce overlap when they 
should simply be next to one another.  The larger the box, the greater the 
probability that this happens.




2012/12/10 francesco oteri 


Hi Mark,
you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
use 0.21. Since I still got errors with this procedure, I decided to remove
water manually through vmd.

Looking carefully at the configurations, I found that the water molecule
originating the error is exactly superimposed to an other molecule so I
simply deleted it and the same error is reported for an other water
molecule.

Although I could scan all the pdb to detect all the superimposed water
molecules, I believed genbox checked for this. Of course the original box
does't contain superimposed molecules.




It is highly unusual for genbox to produce overlapping waters, but per the help 
description, only solute-solvent overlaps are checked, not solvent-solvent, 
which would likely require enormous amounts of memory (and genbox already has 
memory issues).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error with MARTINI depending by the box size

[francesco oteri]

For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before


2012/12/10 francesco oteri 

> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
> water manually through vmd.
>
> Looking carefully at the configurations, I found that the water molecule
> originating the error is exactly superimposed to an other molecule so I
> simply deleted it and the same error is reported for an other water
> molecule.
>
> Although I could scan all the pdb to detect all the superimposed water
> molecules, I believed genbox checked for this. Of course the original box
> does't contain superimposed molecules.
>
>
> Francesco
>
>
> 2012/12/10 Justin Lemkul 
>
>>
>>
>> On 12/10/12 5:15 PM, francesco oteri wrote:
>>
>>> Actually, since I copied and pasted the mail, there is an imprecision.
>>> When
>>> I use 20nm as box side lenght I don't get
>>> any error, everything goes fine.
>>>
>>> I actually tested different size between 19 and 20 nm and I found that
>>> the
>>> minimum size to avoid the error is 19.5nm.
>>> My system has an average size and, as stated by vmd, it size are
>>> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
>>> So a box of 20nm, as well as 19nm, is large enough to accomodate the
>>> protein.
>>>
>>>
>> Those box sizes are vast overkill.  Any reason why you need so much extra
>> water?
>>
>>
>>  Moreover, since I remove the water around the protein (that is already
>>> stabie because of the in vacuo minimization), the problem has to be in
>>> the
>>> bulk water!
>>>
>>>
>> As I said before, you should be able to identify the source of the
>> problem by simple visualization based on what mdrun has told you.
>>
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  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
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Error with MARTINI depending by the box size

[francesco oteri]

Hi Mark,
you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
use 0.21. Since I still got errors with this procedure, I decided to remove
water manually through vmd.

Looking carefully at the configurations, I found that the water molecule
originating the error is exactly superimposed to an other molecule so I
simply deleted it and the same error is reported for an other water
molecule.

Although I could scan all the pdb to detect all the superimposed water
molecules, I believed genbox checked for this. Of course the original box
does't contain superimposed molecules.


Francesco


2012/12/10 Justin Lemkul 

>
>
> On 12/10/12 5:15 PM, francesco oteri wrote:
>
>> Actually, since I copied and pasted the mail, there is an imprecision.
>> When
>> I use 20nm as box side lenght I don't get
>> any error, everything goes fine.
>>
>> I actually tested different size between 19 and 20 nm and I found that the
>> minimum size to avoid the error is 19.5nm.
>> My system has an average size and, as stated by vmd, it size are
>> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
>> So a box of 20nm, as well as 19nm, is large enough to accomodate the
>> protein.
>>
>>
> Those box sizes are vast overkill.  Any reason why you need so much extra
> water?
>
>
>  Moreover, since I remove the water around the protein (that is already
>> stabie because of the in vacuo minimization), the problem has to be in the
>> bulk water!
>>
>>
> As I said before, you should be able to identify the source of the problem
> by simple visualization based on what mdrun has told you.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Error with MARTINI depending by the box size

[Mark Abraham]

On Mon, Dec 10, 2012 at 11:15 PM, francesco oteri  wrote:

> Actually, since I copied and pasted the mail, there is an imprecision. When
> I use 20nm as box side lenght I don't get
> any error, everything goes fine.
>
> I actually tested different size between 19 and 20 nm and I found that the
> minimum size to avoid the error is 19.5nm.
> My system has an average size and, as stated by vmd, it size are
> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
> So a box of 20nm, as well as 19nm, is large enough to accomodate the
> protein.
>

I highly doubt the different sizes are relevant. They're just changing the
starting position enough to make a numerical difference.

Moreover, since I remove the water around the protein (that is already
> stabie because of the in vacuo minimization), the problem has to be in the
> bulk water!
>

Yeah, and since all your stages work in theory, you don't have a problem
:lol:

There's a reason the link I gave has "visualise" as the first diagnostic
suggestion. Your eyes are much better at seeing problems than your brain is
at writing bulletproof scripts.

Mark


>
> Francesco
>
>
> 2012/12/10 Justin Lemkul 
>
> >
> >
> > On 12/10/12 3:48 PM, francesco oteri wrote:
> >
> >> Dear gromacs users,
> >>
> >> I am facing a very tricky problem in building a stable topology.
> >> In particular I am trying to use MARTINI force-field and I noticed that
> if
> >> I use a box whose the side size is smaller than 20nm, the minimization
> >> fails with this message:
> >>
> >> Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
> >> Starting 12 tMPI threads
> >> Using 12 MPI threads
> >> Making 2D domain decomposition 4 x 3 x 1
> >>
> >> Steepest Descents:
> >> Tolerance (Fmax) = 1.0e+03
> >> Number of steps = 2000
> >> Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
> >> Energy minimization has stopped, but the forces havenot converged to the
> >> requested precision Fmax < 1000 (whichmay not be possible for your
> >> system).
> >> It stoppedbecause the algorithm tried to make a new step whose sizewas
> too
> >> small, or there was no change in the energy sincelast step. Either way,
> we
> >> regard the minimization asconverged to within the available machine
> >> precision,given your starting configuration and EM parameters.
> >>
> >> Double precision normally gives you higher accuracy, butthis is often
> not
> >> needed for preparing to run moleculardynamics.
> >> You might need to increase your constraint accuracy, or turn
> >> off constraints altogether (set constraints = none in mdp file)
> >>
> >> writing lowest energy coordinates.
> >>
> >> Steepest Descents converged to machine precision in 15 steps,
> >> but did not reach the requested Fmax < 1000.
> >> Potential Energy = 4.4209897e+18
> >> Maximum force = inf on atom 39063
> >> Norm of force = inf
> >>
> >>
> > With this information, you should be able to deduce the source of the
> > problem.
> >
> >
> >  gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
> >>
> >> But, if I use a box bigger then 19.5nm the minimization, although with
> >> some
> >> LINCS warning, succeeded!
> >>
> >>
> > These LINCS warnings will also give the same information as to where
> > problems start.
> >
> >
> >  I found the problem with gromacs 4.5.5,  4.6beta1 and beta2.
> >>
> >> I am attaching the script (crea_topo.csh) I am using to build the
> >> topologies as well as all the input files you need to replicate the
> error.
> >>
> >> The different topologies have been obtained changing the value of the
> >> variable side in crea_topo.csh
> >>
> >>
> > How many values you have tried?  What is the minimum box size necessary
> to
> > accommodate your system?  This all seems like random failures from
> unstable
> > configurations.
> >
> >
> >  As you can notice from the script, the structure is initially minimized
> in
> >> vacuo to remove problems due in the all atoms-coarse grained
> >> transformation
> >> and then it is solvated, Then, water molecules closer then 0.8nm to
> >> protein
> >> are rmoved through vmd.
> >>
> >>
> > What was the outcome of the in vacuo minimization?
> >
> >
> >  Can you give me some clue on how to solve the problem, except changing
> the
> >> software?.
> >>
> >>
> > http://www.gromacs.org/**Documentation/Terminology/**
> > Blowing_Up#Diagnosing_an_**Unstable_System<
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> >
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-us

Re: [gmx-users] Error with MARTINI depending by the box size

[Justin Lemkul]

On 12/10/12 5:15 PM, francesco oteri wrote:

Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.

I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid the error is 19.5nm.
My system has an average size and, as stated by vmd, it size are
X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
So a box of 20nm, as well as 19nm, is large enough to accomodate the
protein.



Those box sizes are vast overkill.  Any reason why you need so much extra water?


Moreover, since I remove the water around the protein (that is already
stabie because of the in vacuo minimization), the problem has to be in the
bulk water!



As I said before, you should be able to identify the source of the problem by 
simple visualization based on what mdrun has told you.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error with MARTINI depending by the box size

[francesco oteri]

Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.

I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid the error is 19.5nm.
My system has an average size and, as stated by vmd, it size are
X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
So a box of 20nm, as well as 19nm, is large enough to accomodate the
protein.

Moreover, since I remove the water around the protein (that is already
stabie because of the in vacuo minimization), the problem has to be in the
bulk water!

Francesco


2012/12/10 Justin Lemkul 

>
>
> On 12/10/12 3:48 PM, francesco oteri wrote:
>
>> Dear gromacs users,
>>
>> I am facing a very tricky problem in building a stable topology.
>> In particular I am trying to use MARTINI force-field and I noticed that if
>> I use a box whose the side size is smaller than 20nm, the minimization
>> fails with this message:
>>
>> Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
>> Starting 12 tMPI threads
>> Using 12 MPI threads
>> Making 2D domain decomposition 4 x 3 x 1
>>
>> Steepest Descents:
>> Tolerance (Fmax) = 1.0e+03
>> Number of steps = 2000
>> Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
>> Energy minimization has stopped, but the forces havenot converged to the
>> requested precision Fmax < 1000 (whichmay not be possible for your
>> system).
>> It stoppedbecause the algorithm tried to make a new step whose sizewas too
>> small, or there was no change in the energy sincelast step. Either way, we
>> regard the minimization asconverged to within the available machine
>> precision,given your starting configuration and EM parameters.
>>
>> Double precision normally gives you higher accuracy, butthis is often not
>> needed for preparing to run moleculardynamics.
>> You might need to increase your constraint accuracy, or turn
>> off constraints altogether (set constraints = none in mdp file)
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy = 4.4209897e+18
>> Maximum force = inf on atom 39063
>> Norm of force = inf
>>
>>
> With this information, you should be able to deduce the source of the
> problem.
>
>
>  gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
>>
>> But, if I use a box bigger then 19.5nm the minimization, although with
>> some
>> LINCS warning, succeeded!
>>
>>
> These LINCS warnings will also give the same information as to where
> problems start.
>
>
>  I found the problem with gromacs 4.5.5,  4.6beta1 and beta2.
>>
>> I am attaching the script (crea_topo.csh) I am using to build the
>> topologies as well as all the input files you need to replicate the error.
>>
>> The different topologies have been obtained changing the value of the
>> variable side in crea_topo.csh
>>
>>
> How many values you have tried?  What is the minimum box size necessary to
> accommodate your system?  This all seems like random failures from unstable
> configurations.
>
>
>  As you can notice from the script, the structure is initially minimized in
>> vacuo to remove problems due in the all atoms-coarse grained
>> transformation
>> and then it is solvated, Then, water molecules closer then 0.8nm to
>> protein
>> are rmoved through vmd.
>>
>>
> What was the outcome of the in vacuo minimization?
>
>
>  Can you give me some clue on how to solve the problem, except changing the
>> software?.
>>
>>
> http://www.gromacs.org/**Documentation/Terminology/**
> Blowing_Up#Diagnosing_an_**Unstable_System
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  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
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Error with MARTINI depending by the box size

[Mark Abraham]

On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri
wrote:

> Dear gromacs users,
>
> I am facing a very tricky problem in building a stable topology.
> In particular I am trying to use MARTINI force-field and I noticed that if
> I use a box whose the side size is smaller than 20nm, the minimization
> fails with this message:
>
> Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
> Starting 12 tMPI threads
> Using 12 MPI threads
> Making 2D domain decomposition 4 x 3 x 1
>
> Steepest Descents:
> Tolerance (Fmax) = 1.0e+03
> Number of steps = 2000
> Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
> Energy minimization has stopped, but the forces havenot converged to the
> requested precision Fmax < 1000 (whichmay not be possible for your system).
> It stoppedbecause the algorithm tried to make a new step whose sizewas too
> small, or there was no change in the energy sincelast step. Either way, we
> regard the minimization asconverged to within the available machine
> precision,given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, butthis is often not
> needed for preparing to run moleculardynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = 4.4209897e+18
> Maximum force = inf on atom 39063
> Norm of force = inf
>
> gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
>
> But, if I use a box bigger then 19.5nm the minimization, although with some
> LINCS warning, succeeded!
>

The standard advice here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up seems to apply,
because your system also has problems with 4.5.5 and even when it
"succeeds" there is evidence that something is not right (from the LINCS
warnings)


> I found the problem with gromacs 4.5.5,  4.6beta1 and beta2.
>
> I am attaching the script (crea_topo.csh) I am using to build the
> topologies as well as all the input files you need to replicate the error.
>
> The different topologies have been obtained changing the value of the
> variable side in crea_topo.csh
>
> As you can notice from the script, the structure is initially minimized in
> vacuo to remove problems due in the all atoms-coarse grained transformation
> and then it is solvated, Then, water molecules closer then 0.8nm to protein
> are rmoved through vmd.
>
> Can you give me some clue on how to solve the problem, except changing the
> software?.
>

As the above link suggests, make sure you visualize your results. Probably
you will find an ion in an inappropriate place.


>
> I mean, I would like to know whether there is a bug or not in some of the
> program used to build the topology.
>

genion can insert ions of arbitrary name and update the topology in one
step. You don't need your second round of vmd or as much awking.

genbox can do similarly - I'm surprised there's not an existing Martini
workflow that uses genbox -vdwd 0.4 or similar to pre-exclude those waters.

Neither of these is likely your problem, however.

Mark


> Francesco
>
>
>  01em.mdp <
> https://docs.google.com/file/d/0B1ktZ-u2OHFAejUwY2tnQnlnc3c/edit>
>
>  crea_topo.csh<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAcHVZWXJCeXVBc3c/edit>
>
>  Desu_OK.pdb<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAMkRScXlWYWlzMmc/edit>
>
>  dsspcmbi <
> https://docs.google.com/file/d/0B1ktZ-u2OHFAT2hCWVpGWDAwdEU/edit>
>
>  ions.itp <
> https://docs.google.com/file/d/0B1ktZ-u2OHFAYWdpa3o3N09sdEU/edit>
>
>  martini.itp<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAOFVZNkwzN2J3c3c/edit>
>
>  martinize.py<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAZ3hzWnZGcEJyTWM/edit>
>
>  water-1bar-303K.gro<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAcmhMUS1YZEVlUjQ/edit>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Error with MARTINI depending by the box size

[Justin Lemkul]

On 12/10/12 3:48 PM, francesco oteri wrote:

Dear gromacs users,

I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that if
I use a box whose the side size is smaller than 20nm, the minimization
fails with this message:

Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
Starting 12 tMPI threads
Using 12 MPI threads
Making 2D domain decomposition 4 x 3 x 1

Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps = 2000
Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 1000 (whichmay not be possible for your system).
It stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.4209897e+18
Maximum force = inf on atom 39063
Norm of force = inf



With this information, you should be able to deduce the source of the problem.


gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)

But, if I use a box bigger then 19.5nm the minimization, although with some
LINCS warning, succeeded!



These LINCS warnings will also give the same information as to where problems 
start.


I found the problem with gromacs 4.5.5,  4.6beta1 and beta2.

I am attaching the script (crea_topo.csh) I am using to build the
topologies as well as all the input files you need to replicate the error.

The different topologies have been obtained changing the value of the
variable side in crea_topo.csh



How many values you have tried?  What is the minimum box size necessary to 
accommodate your system?  This all seems like random failures from unstable 
configurations.



As you can notice from the script, the structure is initially minimized in
vacuo to remove problems due in the all atoms-coarse grained transformation
and then it is solvated, Then, water molecules closer then 0.8nm to protein
are rmoved through vmd.



What was the outcome of the in vacuo minimization?


Can you give me some clue on how to solve the problem, except changing the
software?.



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

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: What is the purpose of the [ pairs ] section?

[Justin Lemkul]

On 12/10/12 3:13 PM, Andrew DeYoung wrote:

Javier and Mark,

Thank you SO much!  That is so helpful to me.

If you have time, I have two follow-up questions:

(1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified
in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are
provided in [ atomtypes ] in ffnonbonded.itp.

But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a
protein for example?  I think that in OPLS, such interactions are to be
considered at full strength (no scaling down).  My question is: are these
1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions automatically taken
into account if gen-pairs = yes?



Anything beyond a 1-4 interaction is treated as a normal nonbonded interaction 
if nrexcl = 3.  The [pairs] section has no relevance to these unless you hack 
the topology to treat them as such (which you shouldn't).



(2) Suppose that I run grompp (where 1-4 interactions are specified in [
pairs ] and gen-pairs = yes) and grompp gives me the following output:

Generated 276 of the 276 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 276 of the 276 1-4 parameter combinations

Does this output indeed imply that the ONLY nonbonded interactions
considered are 1-4 interactions?  In other words, does this output suggest
that NO 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions are
considered?  If so, why is this the case if I have set gen-pairs = yes?



That output is only relevant to 1-4 interactions.  Since you have gen-pairs = 
yes, then anything not listed in a [pairtypes] directive is generated 
(calculated) from sigma, epsilon, and the fudge factor relevant to the force 
field.  Other force fields use [pairtypes] to specify custom interactions for 
different combinations of atom types.  OPLS-AA is not one of these.


Also, you may find this explanation helpful:

http://lists.gromacs.org/pipermail/gmx-users/2009-July/043326.html

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: What is the purpose of the [ pairs ] section?

[Justin Lemkul]

On 12/10/12 3:27 PM, Andrew DeYoung wrote:

Hi again,

I forgot to mention that in my system I always set nrexcl = 3 (while
explicitly specifying 1-4 interactions in [ pairs ], as I mentioned in my
last message).  Does this mean that if gen-pairs = yes, then 1-5, 1-6, 1-7,
..., 1-Infinity nonbonded interactions will automatically be taken into
account?



They are calculated like any other nonbonded interaction in the system.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: What is the purpose of the [ pairs ] section?

[Andrew DeYoung]

Hi again, 

I forgot to mention that in my system I always set nrexcl = 3 (while
explicitly specifying 1-4 interactions in [ pairs ], as I mentioned in my
last message).  Does this mean that if gen-pairs = yes, then 1-5, 1-6, 1-7,
..., 1-Infinity nonbonded interactions will automatically be taken into
account?

Thank you kindly! 

Andrew DeYoung
Carnegie Mellon University

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[gmx-users] Re: What is the purpose of the [ pairs ] section?

[Andrew DeYoung]

Javier and Mark,

Thank you SO much!  That is so helpful to me.

If you have time, I have two follow-up questions:

(1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified
in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are
provided in [ atomtypes ] in ffnonbonded.itp.

But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a
protein for example?  I think that in OPLS, such interactions are to be
considered at full strength (no scaling down).  My question is: are these
1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions automatically taken
into account if gen-pairs = yes?

(2) Suppose that I run grompp (where 1-4 interactions are specified in [
pairs ] and gen-pairs = yes) and grompp gives me the following output:

Generated 276 of the 276 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 276 of the 276 1-4 parameter combinations

Does this output indeed imply that the ONLY nonbonded interactions
considered are 1-4 interactions?  In other words, does this output suggest
that NO 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions are
considered?  If so, why is this the case if I have set gen-pairs = yes?

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] Pulling ion - US

[Justin Lemkul]

On 12/10/12 10:50 AM, Steven Neumann wrote:

Would you also specify in each US window specific residue instead of
the whole protein?



That really depends on whether the residue-ion distance reflects the desired 
reaction coordinate and if doing so is superior to using the protein-ion 
distance.  The chosen group(s) must define a suitable reaction coordinate for 
the process of interest.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Pulling ion - US

[Steven Neumann]

Would you also specify in each US window specific residue instead of
the whole protein?

Sreven

On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann  wrote:
> On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul  wrote:
>>
>>
>> On 12/10/12 9:01 AM, Steven Neumann wrote:
>>>
>>> Dear Gmx Users,
>>>
>>> I am pulling away cation from the protein glutamic acid residue with:
>>>
>>> pull= umbrella
>>> pull_geometry   = distance  ; simple distance increase
>>> pull_dim= N N Y
>>> pull_start  = yes   ; define initial COM distance > 0
>>> pull_ngroups= 1
>>> pull_group0 = Protein
>>> pull_group1 = NA
>>> pull_rate1  = 0.01
>>> pull_k1 = 500  ; kJ mol^-1 nm^-2
>>>
>>> I tried different pulling rates and simulation time to pull it 3 nm
>>> away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so
>>> strong that the force reaches 600 kJ/mol/nm2 and they do not become
>>> separated - with position restraints protein looses its secondary
>>> structure and is draged by the ion - they do not become separated.
>>>
>>> Would you suggest constant force pulling in this case? Then I will
>>> extract initial coordinates for US windows. Can I use then US with
>>> harmonic potential in windows then and WHAM?
>>>
>>
>> You can generate coordinates in any way you wish.  I would think that,
>> regardless of the pull method, setting pull_group0 to the actual residue to
>> which the ion is coordinated would be significantly more effective than
>> pulling with respect to the entire protein, though it seems rather strange
>> that the dissociation of an ion would cause a protein to unfold.  A stronger
>> force constant in pull_k1 may also help.
>>
>> -Justin
>
> Thank you Justin. That indeed helped.
>
> Steven
>>
>> --
>> 
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
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Re: [gmx-users] Pulling ion - US

[Steven Neumann]

On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul  wrote:
>
>
> On 12/10/12 9:01 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I am pulling away cation from the protein glutamic acid residue with:
>>
>> pull= umbrella
>> pull_geometry   = distance  ; simple distance increase
>> pull_dim= N N Y
>> pull_start  = yes   ; define initial COM distance > 0
>> pull_ngroups= 1
>> pull_group0 = Protein
>> pull_group1 = NA
>> pull_rate1  = 0.01
>> pull_k1 = 500  ; kJ mol^-1 nm^-2
>>
>> I tried different pulling rates and simulation time to pull it 3 nm
>> away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so
>> strong that the force reaches 600 kJ/mol/nm2 and they do not become
>> separated - with position restraints protein looses its secondary
>> structure and is draged by the ion - they do not become separated.
>>
>> Would you suggest constant force pulling in this case? Then I will
>> extract initial coordinates for US windows. Can I use then US with
>> harmonic potential in windows then and WHAM?
>>
>
> You can generate coordinates in any way you wish.  I would think that,
> regardless of the pull method, setting pull_group0 to the actual residue to
> which the ion is coordinated would be significantly more effective than
> pulling with respect to the entire protein, though it seems rather strange
> that the dissociation of an ion would cause a protein to unfold.  A stronger
> force constant in pull_k1 may also help.
>
> -Justin

Thank you Justin. That indeed helped.

Steven
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Center of mass drift in interfacial systems.

[Justin Lemkul]

On 12/10/12 5:18 AM, Anders Lervik wrote:

Dear all,

I have been simulating an inhomogeneous system consisting of a membrane and
a solvent (e.g a lipid bilayer solvated in water). In these simulations, I
have noticed lateral movement in the COMs of the membrane and solvent -
they move in opposite directions such that the overall center of mass of
the system is fixed. A bit of reading on this mailing list tells me that I
should reset the center of mass of the membrane and solvent separately to
avoid this.

I just wonder what the cause of the lateral drift/movement is? Is it a
general "feature" of interfacial systems?




It's certainly normal behavior.  I think Erik hints at the origin of this 
phenomenon here:


http://lists.gromacs.org/pipermail/gmx-users/2005-October/017439.html

If there is no inherent XY friction, then the molecules will move rather freely 
according to their diffusion constants, which for water molecules and lipids 
would be quite different.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Pulling ion - US

[Justin Lemkul]

On 12/10/12 9:01 AM, Steven Neumann wrote:

Dear Gmx Users,

I am pulling away cation from the protein glutamic acid residue with:

pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = NA
pull_rate1  = 0.01
pull_k1 = 500  ; kJ mol^-1 nm^-2

I tried different pulling rates and simulation time to pull it 3 nm
away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so
strong that the force reaches 600 kJ/mol/nm2 and they do not become
separated - with position restraints protein looses its secondary
structure and is draged by the ion - they do not become separated.

Would you suggest constant force pulling in this case? Then I will
extract initial coordinates for US windows. Can I use then US with
harmonic potential in windows then and WHAM?



You can generate coordinates in any way you wish.  I would think that, 
regardless of the pull method, setting pull_group0 to the actual residue to 
which the ion is coordinated would be significantly more effective than pulling 
with respect to the entire protein, though it seems rather strange that the 
dissociation of an ion would cause a protein to unfold.  A stronger force 
constant in pull_k1 may also help.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] What is the purpose of the [ pairs ] section?

[Mark Abraham]

Also, building yourself a test system of (for example) a single amino acid,
varying the .top settings, compiling a .tpr and using mdrun -rerun to
investigate the effects can be a good way to acquire confidence that the
physics you are implementing does match the model you intend.

Mark

On Mon, Dec 10, 2012 at 11:51 AM, Mark Abraham wrote:

> Indeed, thanks Javier.
>
> These kinds of features are a bit awkward to document because there are
> lots of conditions under which various forms of interaction generation are
> used - primarily varying with the forcefield. Different force fields
> motivate various capabilities of pdb2gmx and it's not fully appropriate to
> describe the capabilities without reference to any force fields, nor to
> describe only the capabilities relevant to each force field in turn.
>
> AFAIK section 5.7.1 of the manual has the required information, but some
> of it is buried in the explanation of the worked example. Also, do check
> out the 4.6-beta1 manual http://www.gromacs.org/Documentation/Manual,
> because the tables in 5.7.1 now have cross references to sections (such as
> 5.3.4) to help find the necessary information.
>
> If there's something really missing, do let me know (e.g. via
> http://redmine.gromacs.org/projects/documentation).
>
> Mark
>
>
> On Mon, Dec 10, 2012 at 10:35 AM, Javier Cerezo  wrote:
>
>> Hi
>>
>> The pair section specifies the atoms between which a non-bonded
>> interaction will be build up, even if the "normal" non-bonded is excluded,
>> what is a mechanism to build 1-4 interactions. So, if you want a 1-4
>> interaction to be taken into account, you need to specify it in the
>> topology, in the same way you need to include all bonds, angles...
>>
>> VdW pair interactions should be listed in ffnonbonded.itp, under [
>> pairtypes ] directive, where grompp can find them. However, if such
>> interactions are not there, it is still possible to automatically generate
>> them in the same way as "normal" VdW are generated, and additionally
>> scaling by fudgeLJ. For such pair generation, gen-pairs should be set to
>> yes in [ defaults ], otherwise grompp will give an error if it does not
>> find them in ffnonbonded.itp. Note that if pairs are deffined in
>> ffnonbonded.itp and you set gen-pairs to yes, they will be taken from
>> ffnonbonded.itp.
>>
>> As for coulomb pair interactions, they will be generated only through
>> gen-pairs=yes, as (there is not any directive for them in ffnonbonded.itp),
>> simply scaling the "normal" coulomb by fudgeQQ.
>>
>> So, in the case of OPLS, the resulting 1-4 interactions, providing the [
>> defaults ] that are in forcefield.itp and the fact that there is not [
>> pairtypes ] for this force field, will be those prescribed for the force
>> field, but only if you include the appropriate line under [ pairs ] for all
>> possible combinations.
>>
>> Javier
>>
>> El 08/12/12 23:12, Andrew DeYoung escribió:
>>
>>  Hi,
>>>
>>> I am sure that this is a rather basic question, but I am wondering if you
>>> can please help me to understand something described in the manual.
>>>
>>> What is the purpose of the [ pairs ] section of an .itp file?  What
>>> information does it contain?
>>>
>>> Section 5.3.4 (page 112) of the version 4.5.4 manual says:
>>>
>>> "Extra Lennard-Jones and electrostatic interactions between pairs of
>>> atoms
>>> in a molecule can be added in the [ pairs ] section of a molecule
>>> definition. The parameters for these interactions can be set
>>> independently
>>> from the non-bonded interaction parameters. In the GROMOS force fields,
>>> pairs are only used to modify the 1-4 interactions (interactions of atoms
>>> separated by three bonds). In these force fields the 1-4 interactions are
>>> excluded from the non-bonded interactions (see sec. 5.4)."
>>>
>>> However, I am using the OPLS force field, not GROMOS.  OPLS prescribes
>>> that
>>> 1-4 nonbonded interactions are to be taken at half strength (i.e.,
>>> fudgeQQ =
>>> 0.5 and fudgeLJ = 0.5).  Does this mean that I should specify all
>>> possible
>>> 1-4 nonbonded interactions in the [ pairs ] section?  If I have nrexcl =
>>> 3
>>> specified in [ moleculetype ], then can I assume that 1-5, 1-6, 1-7, etc,
>>> interactions will be taken into account (at full strength), even if such
>>> pairs are not specified in [ pairs ]?  I have set gen-pairs = yes,
>>> fudgeLJ =
>>> 0.5, and fudgeQQ = 0.5.
>>>
>>> Thank you for your time!
>>>
>>> Andrew DeYoung
>>> Carnegie Mellon University
>>>
>>>
>> --
>> Javier CEREZO BASTIDA
>> Ph.D. Student
>> Physical Chemistry
>> Universidad de Murcia
>> 30100, Murcia (SPAIN)
>> T: (0034)868887434
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Plea

Re: [gmx-users] Topolbuild configuration

[Bruce D. Ray]

On Sunday, December 9, 2012 at 7:48 PM SeokYun123  wrote:


>I'm trying to download topolbuild1_2_1 in my Mac computer.


First, why are you using 1.2.1 instead of 1.3 which is also available in the 
user
contributed software section at gromacs.org?  Actually, there should be a
topolbuild1_3_1 contribution there as well.  I don't know what happened
to that release.  Actually, topolbuild is not up to date with gromacs releases.


>I understand that the executable file is in the same directory as the
>Makefile. I also understand the thing about the PATH.


Did you read INSTALLATION.txt in the main directory?


>For different files I have downloaded, I was able to ./configure it and use
>make, but for topolbuild, I wasn't able to ./configure it as it prints out
>an error message.


This is because there isn't a configure script at all for topolbuild
Instead some sample makefiles are provided named Makefile
and Makefile.G4OsX  For your purposes, the supplied Makefile
should work so you just need to type make to get an executable.
Type make clean to clean up afterwards.


>From the previous thread, I read that "Common practice is to then put it in
>some central directory for executables (like /usr/local/bin, or some
>subdirectory of your /home directory, depending on
>your permissions on the system)." 


You can either leave the executable in the src directory where it is built,
or you can move it to a desired directory.  Please remember that the dat
directory contains the parameters files that topolbuild needs in order to
generate a topology.


>I think that would help me fix my problem, but I'm not so sure how to do
>this.
>
>Could anyone give me an advice regarding this issue?

There are  *.txt files in the main directory of each version of topolbuild to
document how to install and how to use the program.  Please remember
that the topologies generated need further editing with a text editor for use
with gromacs 4.5 and 4.6 releases because the organization of topology files
changed with the 4.5 release and topolbuild has not been updated in a while.

 
-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



>
>
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Re: [gmx-users] Scientific notation in .itp files

[Bogdan Costescu]

Hi Andrew!

In addition to Justin's reply, I would like to point out that this is
something you can easily answer yourself by building a few atoms
system using your .itp file and running gmxdump to look at the actual
values stored in the .tpr.

Cheers,
Bogdan

On Sat, Dec 8, 2012 at 6:53 PM, Andrew DeYoung  wrote:
> Hi,
>
> I have been trying to rigorously check my .itp (topology) files for errors.
> Is it true that .itp files allow scientific notation?
>
> For example, suppose that I want to specify sigma = 0.35 nm in
> ffnonbonded.itp.  If I enter either
>
> 3.5e-1
>
> or
>
> 3.5E-1
>
> will these entries indeed specify the value 0.35?  That is, is it true that
> one can use "e" or "E" to specify "times 10 raised to the power"?
>
> Thanks for your time!
>
> Andrew DeYoung
> Carnegie Mellon University
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Re: [gmx-users] What is the purpose of the [ pairs ] section?

[Mark Abraham]

Indeed, thanks Javier.

These kinds of features are a bit awkward to document because there are
lots of conditions under which various forms of interaction generation are
used - primarily varying with the forcefield. Different force fields
motivate various capabilities of pdb2gmx and it's not fully appropriate to
describe the capabilities without reference to any force fields, nor to
describe only the capabilities relevant to each force field in turn.

AFAIK section 5.7.1 of the manual has the required information, but some of
it is buried in the explanation of the worked example. Also, do check out
the 4.6-beta1 manual http://www.gromacs.org/Documentation/Manual, because
the tables in 5.7.1 now have cross references to sections (such as 5.3.4)
to help find the necessary information.

If there's something really missing, do let me know (e.g. via
http://redmine.gromacs.org/projects/documentation).

Mark

On Mon, Dec 10, 2012 at 10:35 AM, Javier Cerezo  wrote:

> Hi
>
> The pair section specifies the atoms between which a non-bonded
> interaction will be build up, even if the "normal" non-bonded is excluded,
> what is a mechanism to build 1-4 interactions. So, if you want a 1-4
> interaction to be taken into account, you need to specify it in the
> topology, in the same way you need to include all bonds, angles...
>
> VdW pair interactions should be listed in ffnonbonded.itp, under [
> pairtypes ] directive, where grompp can find them. However, if such
> interactions are not there, it is still possible to automatically generate
> them in the same way as "normal" VdW are generated, and additionally
> scaling by fudgeLJ. For such pair generation, gen-pairs should be set to
> yes in [ defaults ], otherwise grompp will give an error if it does not
> find them in ffnonbonded.itp. Note that if pairs are deffined in
> ffnonbonded.itp and you set gen-pairs to yes, they will be taken from
> ffnonbonded.itp.
>
> As for coulomb pair interactions, they will be generated only through
> gen-pairs=yes, as (there is not any directive for them in ffnonbonded.itp),
> simply scaling the "normal" coulomb by fudgeQQ.
>
> So, in the case of OPLS, the resulting 1-4 interactions, providing the [
> defaults ] that are in forcefield.itp and the fact that there is not [
> pairtypes ] for this force field, will be those prescribed for the force
> field, but only if you include the appropriate line under [ pairs ] for all
> possible combinations.
>
> Javier
>
> El 08/12/12 23:12, Andrew DeYoung escribió:
>
>  Hi,
>>
>> I am sure that this is a rather basic question, but I am wondering if you
>> can please help me to understand something described in the manual.
>>
>> What is the purpose of the [ pairs ] section of an .itp file?  What
>> information does it contain?
>>
>> Section 5.3.4 (page 112) of the version 4.5.4 manual says:
>>
>> "Extra Lennard-Jones and electrostatic interactions between pairs of atoms
>> in a molecule can be added in the [ pairs ] section of a molecule
>> definition. The parameters for these interactions can be set independently
>> from the non-bonded interaction parameters. In the GROMOS force fields,
>> pairs are only used to modify the 1-4 interactions (interactions of atoms
>> separated by three bonds). In these force fields the 1-4 interactions are
>> excluded from the non-bonded interactions (see sec. 5.4)."
>>
>> However, I am using the OPLS force field, not GROMOS.  OPLS prescribes
>> that
>> 1-4 nonbonded interactions are to be taken at half strength (i.e.,
>> fudgeQQ =
>> 0.5 and fudgeLJ = 0.5).  Does this mean that I should specify all possible
>> 1-4 nonbonded interactions in the [ pairs ] section?  If I have nrexcl = 3
>> specified in [ moleculetype ], then can I assume that 1-5, 1-6, 1-7, etc,
>> interactions will be taken into account (at full strength), even if such
>> pairs are not specified in [ pairs ]?  I have set gen-pairs = yes,
>> fudgeLJ =
>> 0.5, and fudgeQQ = 0.5.
>>
>> Thank you for your time!
>>
>> Andrew DeYoung
>> Carnegie Mellon University
>>
>>
> --
> Javier CEREZO BASTIDA
> Ph.D. Student
> Physical Chemistry
> Universidad de Murcia
> 30100, Murcia (SPAIN)
> T: (0034)868887434
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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[gmx-users] Center of mass drift in interfacial systems.

[Anders Lervik]

Dear all,

I have been simulating an inhomogeneous system consisting of a membrane and
a solvent (e.g a lipid bilayer solvated in water). In these simulations, I
have noticed lateral movement in the COMs of the membrane and solvent -
they move in opposite directions such that the overall center of mass of
the system is fixed. A bit of reading on this mailing list tells me that I
should reset the center of mass of the membrane and solvent separately to
avoid this.

I just wonder what the cause of the lateral drift/movement is? Is it a
general "feature" of interfacial systems?


All the best,
Anders
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Re: [gmx-users] What is the purpose of the [ pairs ] section?

[Javier Cerezo]

Hi

The pair section specifies the atoms between which a non-bonded 
interaction will be build up, even if the "normal" non-bonded is 
excluded, what is a mechanism to build 1-4 interactions. So, if you want 
a 1-4 interaction to be taken into account, you need to specify it in 
the topology, in the same way you need to include all bonds, angles...


VdW pair interactions should be listed in ffnonbonded.itp, under [ 
pairtypes ] directive, where grompp can find them. However, if such 
interactions are not there, it is still possible to automatically 
generate them in the same way as "normal" VdW are generated, and 
additionally scaling by fudgeLJ. For such pair generation, gen-pairs 
should be set to yes in [ defaults ], otherwise grompp will give an 
error if it does not find them in ffnonbonded.itp. Note that if pairs 
are deffined in ffnonbonded.itp and you set gen-pairs to yes, they will 
be taken from ffnonbonded.itp.


As for coulomb pair interactions, they will be generated only through 
gen-pairs=yes, as (there is not any directive for them in 
ffnonbonded.itp), simply scaling the "normal" coulomb by fudgeQQ.


So, in the case of OPLS, the resulting 1-4 interactions, providing the [ 
defaults ] that are in forcefield.itp and the fact that there is not [ 
pairtypes ] for this force field, will be those prescribed for the force 
field, but only if you include the appropriate line under [ pairs ] for 
all possible combinations.


Javier

El 08/12/12 23:12, Andrew DeYoung escribió:

Hi,

I am sure that this is a rather basic question, but I am wondering if you
can please help me to understand something described in the manual.

What is the purpose of the [ pairs ] section of an .itp file?  What
information does it contain?

Section 5.3.4 (page 112) of the version 4.5.4 manual says:

"Extra Lennard-Jones and electrostatic interactions between pairs of atoms
in a molecule can be added in the [ pairs ] section of a molecule
definition. The parameters for these interactions can be set independently
from the non-bonded interaction parameters. In the GROMOS force fields,
pairs are only used to modify the 1-4 interactions (interactions of atoms
separated by three bonds). In these force fields the 1-4 interactions are
excluded from the non-bonded interactions (see sec. 5.4)."

However, I am using the OPLS force field, not GROMOS.  OPLS prescribes that
1-4 nonbonded interactions are to be taken at half strength (i.e., fudgeQQ =
0.5 and fudgeLJ = 0.5).  Does this mean that I should specify all possible
1-4 nonbonded interactions in the [ pairs ] section?  If I have nrexcl = 3
specified in [ moleculetype ], then can I assume that 1-5, 1-6, 1-7, etc,
interactions will be taken into account (at full strength), even if such
pairs are not specified in [ pairs ]?  I have set gen-pairs = yes, fudgeLJ =
0.5, and fudgeQQ = 0.5.

Thank you for your time!

Andrew DeYoung
Carnegie Mellon University



--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434

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Re: [gmx-users] GPU compatibility

[Mark Abraham]

Correct, C1060 does not have the CUDA 2.0 compute capability required for
GROMACS 4.6. We will not have the ability to support GPU cards of lower
capability in the future. Unfortunately, your only GROMACS options are
probably to use the OpenMM functionality in 4.5.x (which is still present
in 4.6, works as far as we know, but is not in our regular test suite and
the feature is probably headed for deprecation). This will not perform as
well as the new native GPU acceleration, and supports a smaller range of
features, but might be better than wasting the GPUs.

Regards,

Mark

On Mon, Dec 10, 2012 at 7:50 AM, Cara Kreck  wrote:

>
>
>
>
> Hi,
>
> We've got a GPU cluster in our group and have really been looking forward
> to running gromacs on it with full functionality. Unfortunately, it looks
> like our NVIDIA Tesla C1060 cards aren't supported by the 4.6 beta. I was
> just wondering if there was any chance that they would be supported in the
> full version? These cards are only a couple of years old now and were
> bought specifically for running MD.
>
> Thanks,
>
> Cara
>
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Re: [gmx-users] Error during compilation of Gromacs-4.5.5

[Mark Abraham]

Hard to say. Your compiler is prehistoric, and things to do with pthreads
are the province of the compiler, so getting a more recent version will
probably fix it.

Mark

On Mon, Dec 10, 2012 at 7:32 AM, BHARATI DUTTA wrote:

> Hi,
>
> The following error pops up during compilation of Gromacs-4.5.5 :
>
> /home/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to
> `pthread_setaffinity_np'. Could you please help me fix it?
>
> I am installing it on
>
> uname -m = x86_64
> uname -r = 2.6.9-5.ELsmp
> uname -s = Linux
> uname -v = #1 SMP Wed Jan 5 19:29:47 EST 2005
> cc (GCC) 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)
>
> glibc : glibc -2.3.4
>
>
>
> Thanks & Regards - Bharati
>
>
> Bharati Dutta
> Research Associate
> Discovery Informatics
> Piramal Life Sciences Limited
> 1, Nirlon Complex,
> Goregaon Link Road,
> Goregaon(E)
> Mumbai, Maharashtra 400 063
> India
> bharati.du...@piramal.com
>
>
>
>
>
> This communication may contain information that is proprietary
> confidential or exempt from disclosure. If you are not the intended
> recipient please note that any other dissemination distribution use or
> copying of this communication is strictly prohibited. Anyone who receives
> this message in error should notify the sender immediately by telephone or
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