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

[XAvier Periole]

I have not followed the thread but concerning the solvation of a  
protein using genbox you need to:
1- use a box of water that has the exact size of the final box you  
want (you make it yourself using any tool you want) and you need to  
define the box size of the protein file as the one of the water box  
conformation. This is given on the last line of the gro file. Then  
genbox -cp -cs should work fine.
2- you need to use a water box size larger than the one you need. This  
solution is generally easier. You can generate a box using genconf - 
nbox option. And again define the box size in the protein conformation  
file and genbox will just do fine.


We generally use -vdwd 0.18. It is a good compromise for disturbing  
the system the least.


Note that these uses have been discussed on the MARTINI forum several  
times.


XAvier.

On Dec 11, 2012, at 9:05 AM, francesco oteri wrote:


Tanks to all for your advices,
I am going to check all the different aspect you suggested and I will
report the results as soon as possible.

Francesco


2012/12/11 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>


==**==

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

[francesco oteri]

Tanks to all for your advices,
I am going to check all the different aspect you suggested and I will
report the results as soon as possible.

Francesco


2012/12/11 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>
> > > * 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>
> > >
> > --
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> > 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 Driv

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>
> > * 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>
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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] 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!
> * 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
>
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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!
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> > * 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.
> * 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 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!
> * 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
>
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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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