Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

*Forgot to comment:*

*So you are saying:  because it is more forgiving, we are observing slab
movement in a run with "com" option for refcoord scaling, and NOT in "all"
option...as such, choosing any one of options "com" or "all" for refcoord
scaling should not matter simulation results point of view, despite of
difference in slab movement observation?*

Thanks
Chetan

On Tue, Jun 17, 2014 at 10:01 AM, Justin Lemkul  wrote:

>
>
> On 6/17/14, 10:32 AM, Chetan Mahajan wrote:
>
>> Any ideas :
>>
>> 1. why slab is moving despite of position constraints?
>>
>>
> Restraints are biasing potentials; they don't prevent movement.  Why is it
> necessary that your slab not move?
>
>
>  2. That too, only with "com" option of refcoord scaling...with "all"
>> option
>> slab does not move...
>>
>>
> Using "all" means the restraint reference for each atom is the original
> position in the input coordinates, with respect to every atom individually.
>  It is more stringent, though it can often be unstable.  The "com" option
> means the restraint potential is calculated with respect to the COM of the
> group of restrained atoms; it is a bit more forgiving, since the COM might
> only move slightly, even if there are relatively larger changes in the
> individual atomic positions.
>
> -Justin
>
>

>  Thanks
>>
>>
>> On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan 
>> wrote:
>>
>>  The pics should be seen in the reverse order. Due to sorting by name,
>>> "After equilibration" pic occurs first.
>>>
>>>
>>> On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan 
>>> wrote:
>>>
>>>  Thanks.
>>>>
>>>> No, same things do not happen when it's a NVT simulation or no mixed
>>>> potentials. Also, with mixed potentials in NPT simulation, this things
>>>> of
>>>> slab moving in one direction (thus following water movement) happens
>>>> only
>>>> with -com option of refcoord-scaling, *not with -all option for
>>>> refcoord-scaling. *
>>>>
>>>>
>>>> I have a crystal slab with equal amount of water on both the sides.
>>>> During NPT equilibration (with refcoord-scaling option of -com, not
>>>> -all),
>>>> some water on side side of the slab enters opposite side due to periodic
>>>> boundary conditions I have (say water on the right side of the slab,
>>>> crosses boundary of the box and enter the left side of the slab due to
>>>> periodic boundaries. Even crystal slab follows this water and move same
>>>> distance in the same direction of water movement. Following link shares
>>>> pictures of the solvated slab before and after equilibration:
>>>>
>>>>
>>>> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
>>>>
>>>> I feel, this is not an error, but it is odd. Due to periodicity we have,
>>>> output of any calculations will remain the same.  Again, with -all
>>>> option
>>>> for refcoord scaling, this movement of water and slab DOES NOT occur.
>>>>
>>>> Thanks a lot!
>>>> regards
>>>> Chetan
>>>>
>>>>
>>>> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham >>> >
>>>> wrote:
>>>>
>>>>  Hi,
>>>>>
>>>>> Repeating myself - simplify things! Do sane things happen with NVT?
>>>>> With
>>>>> no
>>>>> mixed potentials?
>>>>>
>>>>> Your words aren't making sense to me - you'll do much better with
>>>>> pictures,
>>>>> making sure you turn on your visualizer's option to show the periodic
>>>>> box.
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan 
>>>>> wrote:
>>>>>
>>>>>  Hi Justin,
>>>>>>
>>>>>> I, actually, do not want to preserve any voids. Initial void that I
>>>>>> mentioned is supposed to be filled by water during equilibration and
>>>>>> it
>>>>>> does so. However, problem is that some or major quantity of water
>>>>>>
>>>>> moves out
>>>>>
>>>>>> from one side of the box to enter from the opposite side (obeying
>

[gmx-users] Interpreting energy drift

[Chetan Mahajan]

Dear All,

I want to know how to interpret differences in energy drift. I am comparing
energy drifts with respect to position restraints. In system 1, i have
following:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Position Rest.  6782.577.4169.619   -54.0742
 (kJ/mol)

In system 2, I have following:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Position Rest.  6748.74 22165.176   -156.894
 (kJ/mol)

So I understand that energy drift is a energy change artifact due to
numerical integration processes.
I am not sure about the ballpark values.

Which one in above is serious? why?

Thanks
Chetan
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[gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

Dear All,

I am using Berendsen barostat and thermostat for NPT equilibration MD run
at 1 atm and 300 K. While it runs fine, average pressure at the end of the
run is 19 bar. I am confused whether this is way off 1 atm target, or is
justified recalling gromacs manual that says Berendsen barostat does not
yield correct thermodynamic ensemble.

IN addition, initial box elongates to have space at both ends in
z-direction as can be seen in following link:

https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva

Again, I am not sure if this is a case for concern or just artifact of
using Berendsen.

Is Parrinello-Rahman better than Berendsen, even for initial NPT
equilibration?

Thanks
Chetan
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Re: [gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

By space in second part of the email, I meant vacuum.
Thanks
Chetan


On Mon, Jun 23, 2014 at 12:50 AM, Chetan Mahajan 
wrote:

> Dear All,
>
> I am using Berendsen barostat and thermostat for NPT equilibration MD run
> at 1 atm and 300 K. While it runs fine, average pressure at the end of the
> run is 19 bar. I am confused whether this is way off 1 atm target, or is
> justified recalling gromacs manual that says Berendsen barostat does not
> yield correct thermodynamic ensemble.
>
> IN addition, initial box elongates to have space at both ends in
> z-direction as can be seen in following link:
>
> https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva
>
> Again, I am not sure if this is a case for concern or just artifact of
> using Berendsen.
>
> Is Parrinello-Rahman better than Berendsen, even for initial NPT
> equilibration?
>
> Thanks
> Chetan
>
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Re: [gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

Thanks.

Average was taken over 1000 ps. Error estimate is 2.9 which is smaller than
average pressure of 19.87 bar. Here is the complete statistics:

Energy  Average Err.Est.  RMSD  Tot-Drift
---
Temperature  299.968  0.0131.98625   0.062225  (K)
Pressure19.86992.9   726.92413.5906
 (bar)

Interestingly, average pressure is close to one (0.86 or 0.8 bar) when
refcoord scaling of -all is used for position restraints. Above simulation
where average pressure is so large was carried out with refcoord-scaling of
-com option. I am simulating TiO2 crystal solvated by water, formate and
sodium ion. Now, one important observation is that with -com option,
crystal slab moves a distance during change of box dimensions in NPT
equilibration, whereas slab DOES NOT move with -all option. However, -com
option is more favorable since very less water manage to get on the side
surfaces of slab compared to that in -all option, where lot of water get on
the side which is not desirable.

What is happening here? Is it because of slab movement that average
pressure is annoyingly large in simulations with -com option? what can be
done to rectify or is it okay to proceed anyways?

Thanks a lot!
regards
Chetan



On Mon, Jun 23, 2014 at 1:47 AM, Francis Jing  wrote:

> How long was the average taken over? If the error is larger than the
> pressure itself, you cannot make judgment.
> Generally Berendsen is only inaccurate about the fluctuations, not the mean
> value.
>
>
> Francis
>
>
> On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan 
> wrote:
>
> > Dear All,
> >
> > I am using Berendsen barostat and thermostat for NPT equilibration MD run
> > at 1 atm and 300 K. While it runs fine, average pressure at the end of
> the
> > run is 19 bar. I am confused whether this is way off 1 atm target, or is
> > justified recalling gromacs manual that says Berendsen barostat does not
> > yield correct thermodynamic ensemble.
> >
> > IN addition, initial box elongates to have space at both ends in
> > z-direction as can be seen in following link:
> >
> > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva
> >
> > Again, I am not sure if this is a case for concern or just artifact of
> > using Berendsen.
> >
> > Is Parrinello-Rahman better than Berendsen, even for initial NPT
> > equilibration?
> >
> > Thanks
> > Chetan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Zhifeng (Francis) Jing
> Graduate Student in Physical Chemistry
> School of Chemistry and Chemical Engineering
> Shanghai Jiao Tong University
> http://sun.sjtu.edu.cn
> --
> Gromacs Users mailing list
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Re: [gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

Thank  you, Dr. Shirts. My pressure coupling type is also semi-isotropic.
So is that simulation worth at all  ( since equilibration not on intended
pressure even remotely) or we need to discard the simulation totally ?

Also, this high pressure (and crystal slab movement ) occurs only with
refcoord-scaling option of -com and not with -all. I wonder why.

Thanks.

regards
Chetan

On Mon, Jun 23, 2014 at 3:35 PM, Michael Shirts  wrote:

> A nonisotropic system will not necessarily end up with exactly the applied
> pressure -- things like surface tension and stresses/strains end up getting
> mixed in and throwing things off.
>
>
> On Mon, Jun 23, 2014 at 3:32 PM, Chetan Mahajan 
> wrote:
>
> > Thanks.
> >
> > Average was taken over 1000 ps. Error estimate is 2.9 which is smaller
> than
> > average pressure of 19.87 bar. Here is the complete statistics:
> >
> > Energy  Average Err.Est.  RMSD  Tot-Drift
> >
> >
> ---
> > Temperature  299.968  0.0131.98625   0.062225  (K)
> > Pressure19.86992.9   726.92413.5906
> >  (bar)
> >
> > Interestingly, average pressure is close to one (0.86 or 0.8 bar) when
> > refcoord scaling of -all is used for position restraints. Above
> simulation
> > where average pressure is so large was carried out with refcoord-scaling
> of
> > -com option. I am simulating TiO2 crystal solvated by water, formate and
> > sodium ion. Now, one important observation is that with -com option,
> > crystal slab moves a distance during change of box dimensions in NPT
> > equilibration, whereas slab DOES NOT move with -all option. However, -com
> > option is more favorable since very less water manage to get on the side
> > surfaces of slab compared to that in -all option, where lot of water get
> on
> > the side which is not desirable.
> >
> > What is happening here? Is it because of slab movement that average
> > pressure is annoyingly large in simulations with -com option? what can be
> > done to rectify or is it okay to proceed anyways?
> >
> > Thanks a lot!
> > regards
> > Chetan
> >
> >
> >
> > On Mon, Jun 23, 2014 at 1:47 AM, Francis Jing 
> > wrote:
> >
> > > How long was the average taken over? If the error is larger than the
> > > pressure itself, you cannot make judgment.
> > > Generally Berendsen is only inaccurate about the fluctuations, not the
> > mean
> > > value.
> > >
> > >
> > > Francis
> > >
> > >
> > > On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan 
> > > wrote:
> > >
> > > > Dear All,
> > > >
> > > > I am using Berendsen barostat and thermostat for NPT equilibration MD
> > run
> > > > at 1 atm and 300 K. While it runs fine, average pressure at the end
> of
> > > the
> > > > run is 19 bar. I am confused whether this is way off 1 atm target, or
> > is
> > > > justified recalling gromacs manual that says Berendsen barostat does
> > not
> > > > yield correct thermodynamic ensemble.
> > > >
> > > > IN addition, initial box elongates to have space at both ends in
> > > > z-direction as can be seen in following link:
> > > >
> > > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva
> > > >
> > > > Again, I am not sure if this is a case for concern or just artifact
> of
> > > > using Berendsen.
> > > >
> > > > Is Parrinello-Rahman better than Berendsen, even for initial NPT
> > > > equilibration?
> > > >
> > > > Thanks
> > > > Chetan
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Zhifeng (Francis) Jing
> > > Graduate Student in Physical Chemistry
> > > School of Chemistry and Chemical Engineering
> > &g

[gmx-users] no domain decomposition

[Chetan Mahajan]

Hello,

I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in
my system. I am getting following error:


Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 1.81239 nm
Change the number of nodes or mdrun option -rdd

 Following is an excerpt of log file:

Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163
  multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163
Minimum cell size due to bonded interactions: 1.812 nm
Using 0 separate PME nodes, as there are too few total
 nodes for efficient splitting
Optimizing the DD grid for 16 cells with a minimum initial size of 1.812 nm
The maximum allowed number of cells is: X 1 Y 1 Z 6


*I tried decreasing number of nodes from 48 to 16, but this error appears
always. 2161 and 2163 atoms mentioned in log file excerpt above are formate
atoms each of which is in a different charge group. I can't put them in
same charge group, since they are different energy groups as we can see. *

*Any suggestions how to interpret log file excerpt or what more can be
done?*

Thanks
Chetan
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Re: [gmx-users] no domain decomposition

[Chetan Mahajan]

Thanks, Mark. I was translating a crystal and for some reason, C atom of
formate was getting displaced. Now, it's working.


On Wed, Jun 25, 2014 at 7:16 AM, Mark Abraham 
wrote:

> Why do you have a bonded interaction whose length is 1.6nm? Mdrun is
> telling you that is limiting you.
>
> Mark
> On Jun 25, 2014 12:26 PM, "Chetan Mahajan"  wrote:
>
> > Hello,
> >
> > I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water)
> in
> > my system. I am getting following error:
> >
> >
> > Fatal error:
> > There is no domain decomposition for 16 nodes that is compatible with the
> > given box and a minimum cell size of 1.81239 nm
> > Change the number of nodes or mdrun option -rdd
> >
> >  Following is an excerpt of log file:
> >
> > Initializing Domain Decomposition on 16 nodes
> > Dynamic load balancing: no
> > Will sort the charge groups at every domain (re)decomposition
> > Initial maximum inter charge-group distances:
> > two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163
> >   multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163
> > Minimum cell size due to bonded interactions: 1.812 nm
> > Using 0 separate PME nodes, as there are too few total
> >  nodes for efficient splitting
> > Optimizing the DD grid for 16 cells with a minimum initial size of 1.812
> nm
> > The maximum allowed number of cells is: X 1 Y 1 Z 6
> >
> >
> > *I tried decreasing number of nodes from 48 to 16, but this error appears
> > always. 2161 and 2163 atoms mentioned in log file excerpt above are
> formate
> > atoms each of which is in a different charge group. I can't put them in
> > same charge group, since they are different energy groups as we can see.
> *
> >
> > *Any suggestions how to interpret log file excerpt or what more can be
> > done?*
> >
> > Thanks
> > Chetan
> > --
> > Gromacs Users mailing list
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> > posting!
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[gmx-users] gromacs genbox SPC water population

[Chetan Mahajan]

Dear All,

I have a system of a crystal slab at the center of the box surrounded by
water. I am using position restraints for crystal. I am observing a weird
thing that after NPT equilibration of system populated with SPC water using
gromacs genbox command, some kinda hole or vacuum appears in the water
layers. Let me explain with the snapshots that can be accessed from
following link:

https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa

Image 1 shows equilibrated snapshot of system with "all" as refcoord
scaling option and water NOT from genbox command, but instead inserted
manually. As we can see, there are no holes/vacuum in the box.

Images 2 and 3 show the holes in the water layers. refcoord scaling option
"all" is used and crystal is solvated by SPC water, latter generated using
genbox command.

Image 4 shows equilibrated snapshot of system where "com" option is used
for refcoord scaling, and crystal is populated with SPC water from genbox
command. As we see, there is a displacement of the slab from center to
left, but there are no holes/vacuum in the water layers.

Thus, combination of all option and genbox SPC population is problematic
for some reason. Noting that slab does not move with "all" option, whereas
it does move with "com" option, there is some issue with SPC water
generation using genbox in gromacs. Also, I am using following settle
algorithm for constraining water geometry:

[ settles ]
; i   funct   length-oh length -hh
  110.1  0.16333

 Could anyone shed light?

Thanks a lot!

regards
Chetan
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Re: [gmx-users] gromacs genbox SPC water population

[Chetan Mahajan]

Just to be complete: I am using following command to populate system with
SPC water using genbox:

genbox -cp slab_wligf.gro -cs spc216.gro -vdwd 0.5 -box 3.081 3.637 11.07514

Thanks
Chetan


On Wed, Jun 25, 2014 at 7:48 PM, Chetan Mahajan 
wrote:

> Dear All,
>
> I have a system of a crystal slab at the center of the box surrounded by
> water. I am using position restraints for crystal. I am observing a weird
> thing that after NPT equilibration of system populated with SPC water using
> gromacs genbox command, some kinda hole or vacuum appears in the water
> layers. Let me explain with the snapshots that can be accessed from
> following link:
>
> https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa
>
> Image 1 shows equilibrated snapshot of system with "all" as refcoord
> scaling option and water NOT from genbox command, but instead inserted
> manually. As we can see, there are no holes/vacuum in the box.
>
> Images 2 and 3 show the holes in the water layers. refcoord scaling option
> "all" is used and crystal is solvated by SPC water, latter generated using
> genbox command.
>
> Image 4 shows equilibrated snapshot of system where "com" option is used
> for refcoord scaling, and crystal is populated with SPC water from genbox
> command. As we see, there is a displacement of the slab from center to
> left, but there are no holes/vacuum in the water layers.
>
> Thus, combination of all option and genbox SPC population is problematic
> for some reason. Noting that slab does not move with "all" option, whereas
> it does move with "com" option, there is some issue with SPC water
> generation using genbox in gromacs. Also, I am using following settle
> algorithm for constraining water geometry:
>
> [ settles ]
> ; i   funct   length-oh length -hh
>   110.1  0.16333
>
>  Could anyone shed light?
>
> Thanks a lot!
>
> regards
> Chetan
>
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Re: [gmx-users] gromacs genbox SPC water population

[Chetan Mahajan]

I have solved this problem, by letting -vdwd option of genbox take its
default value rather than my first value of 0.55.
Thanks
Chetan


On Wed, Jun 25, 2014 at 7:52 PM, Chetan Mahajan 
wrote:

> Just to be complete: I am using following command to populate system with
> SPC water using genbox:
>
> genbox -cp slab_wligf.gro -cs spc216.gro -vdwd 0.5 -box 3.081 3.637
> 11.07514
>
> Thanks
> Chetan
>
>
> On Wed, Jun 25, 2014 at 7:48 PM, Chetan Mahajan 
> wrote:
>
>> Dear All,
>>
>> I have a system of a crystal slab at the center of the box surrounded by
>> water. I am using position restraints for crystal. I am observing a weird
>> thing that after NPT equilibration of system populated with SPC water using
>> gromacs genbox command, some kinda hole or vacuum appears in the water
>> layers. Let me explain with the snapshots that can be accessed from
>> following link:
>>
>> https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa
>>
>> Image 1 shows equilibrated snapshot of system with "all" as refcoord
>> scaling option and water NOT from genbox command, but instead inserted
>> manually. As we can see, there are no holes/vacuum in the box.
>>
>> Images 2 and 3 show the holes in the water layers. refcoord scaling
>> option "all" is used and crystal is solvated by SPC water, latter generated
>> using genbox command.
>>
>> Image 4 shows equilibrated snapshot of system where "com" option is used
>> for refcoord scaling, and crystal is populated with SPC water from genbox
>> command. As we see, there is a displacement of the slab from center to
>> left, but there are no holes/vacuum in the water layers.
>>
>> Thus, combination of all option and genbox SPC population is problematic
>> for some reason. Noting that slab does not move with "all" option, whereas
>> it does move with "com" option, there is some issue with SPC water
>> generation using genbox in gromacs. Also, I am using following settle
>> algorithm for constraining water geometry:
>>
>> [ settles ]
>> ; i   funct   length-oh length -hh
>>   110.1  0.16333
>>
>>  Could anyone shed light?
>>
>> Thanks a lot!
>>
>> regards
>> Chetan
>>
>
>
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[gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

Dear All,

I need some help to generate .gro file corresponding to a given timeframe
of the trajectory obtained in gromacs MD run.

Currently, I am using following command to generate a .gro timeframe (5000
ps) from .xtc trajectory:


*trjconv -f lnanop.xtc -o time5000.gro -s lnanop.tpr -dump 5000*

where lnanop.tpr is generated by following command at the beginning of the
MD run which geenrates above .xtc file:

grompp -f $sethome/prod_lnanopff16.mdp -c $b4prod/lnanop.gro -p
$sethome/outff18-2_aftermin.top -o lnanop.tpr -n $sethome/index18-2.ndx

where each file means by what is implied by its extension.

Now, the comparison of input file to grompp and time0.gro (initial)
timeframe generated by "trjconv" command on .xtc looks good. However, there
are some differences between the files lnanop.gro (generated at the end of
the gromacs MD run) and that generated from "trjconv" command to extract
last timeframe of the same xtc trajectory, *although files match on many
other accounts. Some of the output of -diff command on two files in the
following*:

@@ -2322,8 +2322,8 @@
55SOLHW1 2320   3.174   0.144   7.460
55SOLHW2 2321   3.041   0.201   7.382
56SOL OW 2322   0.015   1.114   1.210
*-   56SOLHW1 2323  -0.031   1.076   1.130 *
*-   56SOLHW2 2324  -0.040   1.096   1.292 *
*+   56SOLHW1 2323   3.191   1.076   1.130*
*+   56SOLHW2 2324   3.182   1.096   1.292*
57SOL OW 2325   1.398   3.388  10.246
57SOLHW1 2326   1.471   3.321  10.236
57SOLHW2 2327   1.365   3.388  10.341

- : for .gro file at the end of gromacs MD run
+ : for .gro timeframe file obtained from .xtc trajectory ( using trjconv):
that with no signs, is the common part of the two files

What's happening? Please comment. Thanks a lot!

regards
Chetan
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Re: [gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
from xtc trajectory are not wrapped, whereas those in the .gro file
generated at the end of gromacs MD run are wrapped in the box?

Now I have a question:  the negative coordinates that are present in the
following text are from .gro file (generated at the end of MD run), whereas
positive ones are from .gro file obtained using trjconv on xtc.

Thanks
Chetan


On Tue, Jul 1, 2014 at 7:57 PM, Justin Lemkul  wrote:

>
>
> On 7/1/14, 8:53 PM, Chetan Mahajan wrote:
>
>> Dear All,
>>
>> I need some help to generate .gro file corresponding to a given timeframe
>> of the trajectory obtained in gromacs MD run.
>>
>> Currently, I am using following command to generate a .gro timeframe (5000
>> ps) from .xtc trajectory:
>>
>>
>> *trjconv -f lnanop.xtc -o time5000.gro -s lnanop.tpr -dump 5000*
>>
>>
>> where lnanop.tpr is generated by following command at the beginning of the
>> MD run which geenrates above .xtc file:
>>
>> grompp -f $sethome/prod_lnanopff16.mdp -c $b4prod/lnanop.gro -p
>> $sethome/outff18-2_aftermin.top -o lnanop.tpr -n $sethome/index18-2.ndx
>>
>> where each file means by what is implied by its extension.
>>
>> Now, the comparison of input file to grompp and time0.gro (initial)
>> timeframe generated by "trjconv" command on .xtc looks good. However,
>> there
>> are some differences between the files lnanop.gro (generated at the end of
>> the gromacs MD run) and that generated from "trjconv" command to extract
>> last timeframe of the same xtc trajectory, *although files match on many
>>
>> other accounts. Some of the output of -diff command on two files in the
>> following*:
>>
>>
>> @@ -2322,8 +2322,8 @@
>>  55SOLHW1 2320   3.174   0.144   7.460
>>  55SOLHW2 2321   3.041   0.201   7.382
>>  56SOL OW 2322   0.015   1.114   1.210
>> *-   56SOLHW1 2323  -0.031   1.076   1.130 *
>> *-   56SOLHW2 2324  -0.040   1.096   1.292 *
>> *+   56SOLHW1 2323   3.191   1.076   1.130*
>> *+   56SOLHW2 2324   3.182   1.096   1.292*
>>
>>  57SOL OW 2325   1.398   3.388  10.246
>>  57SOLHW1 2326   1.471   3.321  10.236
>>  57SOLHW2 2327   1.365   3.388  10.341
>>
>> - : for .gro file at the end of gromacs MD run
>> + : for .gro timeframe file obtained from .xtc trajectory ( using
>> trjconv):
>> that with no signs, is the common part of the two files
>>
>> What's happening? Please comment. Thanks a lot!
>>
>>
> Periodicity.  The final configuration is "made whole" and atoms are put in
> the box such that they have positive coordinates.  The frames within the
> .xtc file are not whole and not corrected for any particular convention.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

Thanks, Justin. *Until now, I was thinking that xtc coordinates are
wrapped. It's good to know that coordinates from xtc files are unwrapped
(please comment if not correct, since we talked only with respect to gro
file). *But I am confused at another thing. I have known at the origin of
the box is at one of its vertices ( is that not true?). *Then why are some
coordinates in .gro file (the one generated at the end of gromacs MD run)
negative, if coordinates are wrapped in the box?*

Is my original command using trjconv okay?

Whereas I do get a sample x-coordinate in .gro file, generated at the end
of MD run (let's call it gro1) from that in .gro file, generated using
trjconv on xtc (let's call it gro2) by adding a box length to concerned
coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a
boxlength that we interconvert between similar values, as shown in excerpt
2 of the SAME file. *Why is there no consistency of conversion between SAME
two .gro files for all the coordinates? How do I mathematically obtain file
2 from file 1 with some consistent measure?  *

- : for .gro file at the end of gromacs MD run (gro1)
+ : for .gro timeframe file obtained from .xtc trajectory ( using trjconv)
(gro2)

*EXCERT 1*

-   11SOLHW1 2188   3.244   3.071  10.934
-   11SOLHW2 2189   3.211   2.940  10.842
+   11SOLHW1 2188   0.023   3.071  10.934
+   11SOLHW2 2189  -0.011   2.940  10.842


*EXCERT 2*
-   56SOLHW1 2323  -0.031   1.076   1.130
-   56SOLHW2 2324  -0.040   1.096   1.292
+   56SOLHW1 2323   3.191   1.076   1.130
+   56SOLHW2 2324   3.182   1.096   1.292

Thanks
Chetan

On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul  wrote:

>
>
> On 7/1/14, 9:08 PM, Chetan Mahajan wrote:
>
>> Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
>> from xtc trajectory are not wrapped, whereas those in the .gro file
>> generated at the end of gromacs MD run are wrapped in the box?
>>
>>
> Yes, unless you've manipulated the trajectory in some way with trjconv
> beforehand.
>
>
>  Now I have a question:  the negative coordinates that are present in the
>> following text are from .gro file (generated at the end of MD run),
>> whereas
>> positive ones are from .gro file obtained using trjconv on xtc.
>>
>>
> Either way, it's a periodicity effect.  Molecules are made whole.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be seen in the following snapshot? I would
expect many of them scattered in space, beyond original box?

https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va

Dark blue line is the box boundary.

Thanks
Chetan


On Wed, Jul 2, 2014 at 5:14 AM, Justin Lemkul  wrote:

>
>
> On 7/1/14, 11:28 PM, Chetan Mahajan wrote:
>
>> Thanks, Justin. *Until now, I was thinking that xtc coordinates are
>>
>> wrapped. It's good to know that coordinates from xtc files are unwrapped
>> (please comment if not correct, since we talked only with respect to gro
>>
>
> That is correct.  mdrun doesn't care about our visualization convenience.
>  No sense in wasting performance doing imaging on the fly when it's not
> necessary.
>
>  file). *But I am confused at another thing. I have known at the origin of
>> the box is at one of its vertices ( is that not true?). *Then why are some
>>
>> coordinates in .gro file (the one generated at the end of gromacs MD run)
>> negative, if coordinates are wrapped in the box?*
>>
>>
> Molecules are made whole; sometimes they're translated in the positive
> direction, sometimes in the negative direction, depending on how the
> molecule is being reconstructed.
>
>
>  Is my original command using trjconv okay?
>>
>>
> "OK" is relative.  In this case, you seem troubled by the slight
> difference in convention, but there's nothing "wrong" with the command.  If
> you want trjconv to make molecules whole, use -pbc mol or -pbc whole.  Your
> original command simply dumps the coordinates and does nothing about
> periodicity.
>
>  Whereas I do get a sample x-coordinate in .gro file, generated at the end
>> of MD run (let's call it gro1) from that in .gro file, generated using
>> trjconv on xtc (let's call it gro2) by adding a box length to concerned
>> coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a
>> boxlength that we interconvert between similar values, as shown in excerpt
>> 2 of the SAME file. *Why is there no consistency of conversion between
>> SAME
>>
>> two .gro files for all the coordinates? How do I mathematically obtain
>> file
>> 2 from file 1 with some consistent measure?  *
>>
>>
> See above.  trjconv will do it for you.
>
> -Justin
>
>  - : for .gro file at the end of gromacs MD run (gro1)
>> + : for .gro timeframe file obtained from .xtc trajectory ( using trjconv)
>> (gro2)
>>
>> *EXCERT 1*
>>
>>
>> -   11SOLHW1 2188   3.244   3.071  10.934
>> -   11SOLHW2 2189   3.211   2.940  10.842
>> +   11SOLHW1 2188   0.023   3.071  10.934
>> +   11SOLHW2 2189  -0.011   2.940  10.842
>>
>>
>> *EXCERT 2*
>>
>> -   56SOLHW1 2323  -0.031   1.076   1.130
>> -   56SOLHW2 2324  -0.040   1.096   1.292
>> +   56SOLHW1 2323   3.191   1.076   1.130
>> +   56SOLHW2 2324   3.182   1.096   1.292
>>
>> Thanks
>> Chetan
>>
>> On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/1/14, 9:08 PM, Chetan Mahajan wrote:
>>>
>>>  Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
>>>> from xtc trajectory are not wrapped, whereas those in the .gro file
>>>> generated at the end of gromacs MD run are wrapped in the box?
>>>>
>>>>
>>>>  Yes, unless you've manipulated the trajectory in some way with trjconv
>>> beforehand.
>>>
>>>
>>>   Now I have a question:  the negative coordinates that are present in
>>> the
>>>
>>>> following text are from .gro file (generated at the end of MD run),
>>>> whereas
>>>> positive ones are from .gro file obtained using trjconv on xtc.
>>>>
>>>>
>>>>  Either way, it's a periodicity effect.  Molecules are made whole.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 2

[gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Dear All,

I recently made a molecular dynamics run of TiO2-water-sodium-formate
system of 12740 atoms. Then I extracted dump file from xtc file of
production run ( NPT, 300 K, 1 bar) using gmxdump command. THere are total
10001 frames. Now, I have found that some quote ( not error/warning) is
getting printed in the middle of the listed coordinates of last frame (end
of NPT run) in dump file, following quote gets printed:

   x[ 3129]={ 1.14500e+00,  3.43700e+00,  1.79100e+00}
   x[ 3130]={ 1.06200e+00,  3.30200e+00,  1.82800e+00}

gcq#252: "This is Tense !" (Star Wars Episode I The Phantom Menace)

  x[ 3131]={ 2.03000e-01,  2.49500e+00,  8.39800e+00}
x[ 3132]={ 1.98000e-01,  2.54600e+00,  8.31200e+00}
x[ 3133]={ 2.76000e-01,  2.53300e+00,  8.45500e+00}

Can anyone explain what's going on? How to correct this? I do not see any
errors or warnings in output file.  Following is the .mdp file of
production run, if anyone wants to have a look:

integrator   = md-vv
dt   = 0.002
nsteps   = 250
nstxout  = 1000
nstvout  = 1000
nstlog   = 1000
nstenergy= 1000
nstxtcout= 250
nstlist  = 1
ns-type  = grid
rlist= 1.0
vdwtype  = user
coulombtype  = pme
rcoulomb = 1.0
rvdw = 1.0
energygrps   = Ti OT OW c h5 o HW Na
energygrp-table  = Ti Ti OT OT Ti OT Ti OW OT c OT h5 OT o
tcoupl   = nose-hoover
tc-grps  = System
tau-t= 0.5
ref-t= 300
pcoupl   = no


Thanks
Chetan
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Re: [gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Thanks, Justin and Roland. While 2>/dev/null/ at the end of gmxdump command
removes that quote nicely, adding either of following commands fails. I am
using gromacs 4.6.5.:

Following did not work ( why? curious since above 2>/dev/null/ will
suppress all errors getting displayed)

1. GMX_NO_QUOTES = 1
gmxdump -f lnanop.xtc

2. gmxdump -f lnanop.xtc -quiet

Thanks
Chetan


On Mon, Jul 7, 2014 at 7:07 PM, Justin Lemkul  wrote:

>
>
> On 7/7/14, 6:28 PM, Chetan Mahajan wrote:
>
>> Dear All,
>>
>> I recently made a molecular dynamics run of TiO2-water-sodium-formate
>> system of 12740 atoms. Then I extracted dump file from xtc file of
>> production run ( NPT, 300 K, 1 bar) using gmxdump command. THere are total
>> 10001 frames. Now, I have found that some quote ( not error/warning) is
>> getting printed in the middle of the listed coordinates of last frame (end
>> of NPT run) in dump file, following quote gets printed:
>>
>> x[ 3129]={ 1.14500e+00,  3.43700e+00,  1.79100e+00}
>> x[ 3130]={ 1.06200e+00,  3.30200e+00,  1.82800e+00}
>>
>> gcq#252: "This is Tense !" (Star Wars Episode I The Phantom Menace)
>>
>>
> gcq = Gromacs Cool Quotes, witty little quips that are intended to augment
> your enjoyment of using Gromacs.  If you don't want to see them printed,
> use -quiet, use the GMX_NO_QUOTES environment variables, or disable when
> configuring with cmake -DGMX_COOL_QUOTES=OFF.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
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Re: [gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Thanks, Justin. GMX_NO_QUOTES is working and there is no such quote, but a
different message at the same place:

Thanx for Using GROMACS - Have a Nice Day

Why are such messages ( even previous ones) appearing in the middle of
coordinates, although from last timeframe?

Thanks
Chetan




On Mon, Jul 7, 2014 at 8:10 PM, Justin Lemkul  wrote:

>
>
> On 7/7/14, 9:06 PM, Chetan Mahajan wrote:
>
>> Thanks, Justin and Roland. While 2>/dev/null/ at the end of gmxdump
>> command
>> removes that quote nicely, adding either of following commands fails. I am
>> using gromacs 4.6.5.:
>>
>> Following did not work ( why? curious since above 2>/dev/null/ will
>> suppress all errors getting displayed)
>>
>> 1. GMX_NO_QUOTES = 1
>> gmxdump -f lnanop.xtc
>>
>>
> Incorrect syntax.
>
> export GMX_NO_QUOTES=1
>
>
>  2. gmxdump -f lnanop.xtc -quiet
>>
>>
> The -quiet option will suppress quotes in 5.0, not 4.6.5, as Roland said.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Hi Tsjerk,

Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end of
the command seems the only way out, since, as I said, I am also getting
greeting messages in addition to gcq quotes. However, adding  2>/dev/null  will
also suppress unusual errors, if any at all. There does not seem a way out
of this.

Thanks
Chetan


On Tue, Jul 8, 2014 at 1:14 AM, Tsjerk Wassenaar  wrote:

> Hi Chetan,
>
> A file has two terminal output streams: stdout, which is buffered, and
> stderr, which is unbuffered. The messages are written to stderr and printed
> as soon as they are received. The coordinates and such are collected until
> the buffer is full and then printed, or printed upon exit of the program.
> the latter accounts for the quote appearing in the middle of your output.
>
> Cheers,
>
> Tsjerk
> On Jul 8, 2014 5:06 AM, "Chetan Mahajan"  wrote:
>
> > Thanks, Justin. GMX_NO_QUOTES is working and there is no such quote, but
> a
> > different message at the same place:
> >
> > Thanx for Using GROMACS - Have a Nice Day
> >
> > Why are such messages ( even previous ones) appearing in the middle of
> > coordinates, although from last timeframe?
> >
> > Thanks
> > Chetan
> >
> >
> >
> >
> > On Mon, Jul 7, 2014 at 8:10 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/7/14, 9:06 PM, Chetan Mahajan wrote:
> > >
> > >> Thanks, Justin and Roland. While 2>/dev/null/ at the end of gmxdump
> > >> command
> > >> removes that quote nicely, adding either of following commands fails.
> I
> > am
> > >> using gromacs 4.6.5.:
> > >>
> > >> Following did not work ( why? curious since above 2>/dev/null/ will
> > >> suppress all errors getting displayed)
> > >>
> > >> 1. GMX_NO_QUOTES = 1
> > >> gmxdump -f lnanop.xtc
> > >>
> > >>
> > > Incorrect syntax.
> > >
> > > export GMX_NO_QUOTES=1
> > >
> > >
> > >  2. gmxdump -f lnanop.xtc -quiet
> > >>
> > >>
> > > The -quiet option will suppress quotes in 5.0, not 4.6.5, as Roland
> said.
> > >
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Thanks, Tsjerk. Got to focus on unix sometime :-)


On Tue, Jul 8, 2014 at 11:58 AM, Tsjerk Wassenaar  wrote:

> Hi Chetan,
>
> You can write the error stream to file: 2>stderr.log
> That way, you can check afterwards.
>
> Cheers,
>
> Tsjerk
> On Jul 8, 2014 6:45 PM, "Chetan Mahajan"  wrote:
>
> > Hi Tsjerk,
> >
> > Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end of
> > the command seems the only way out, since, as I said, I am also getting
> > greeting messages in addition to gcq quotes. However, adding  2>/dev/null
> >  will
> > also suppress unusual errors, if any at all. There does not seem a way
> out
> > of this.
> >
> > Thanks
> > Chetan
> >
> >
> > On Tue, Jul 8, 2014 at 1:14 AM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi Chetan,
> > >
> > > A file has two terminal output streams: stdout, which is buffered, and
> > > stderr, which is unbuffered. The messages are written to stderr and
> > printed
> > > as soon as they are received. The coordinates and such are collected
> > until
> > > the buffer is full and then printed, or printed upon exit of the
> program.
> > > the latter accounts for the quote appearing in the middle of your
> output.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > > On Jul 8, 2014 5:06 AM, "Chetan Mahajan"  wrote:
> > >
> > > > Thanks, Justin. GMX_NO_QUOTES is working and there is no such quote,
> > but
> > > a
> > > > different message at the same place:
> > > >
> > > > Thanx for Using GROMACS - Have a Nice Day
> > > >
> > > > Why are such messages ( even previous ones) appearing in the middle
> of
> > > > coordinates, although from last timeframe?
> > > >
> > > > Thanks
> > > > Chetan
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, Jul 7, 2014 at 8:10 PM, Justin Lemkul 
> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 7/7/14, 9:06 PM, Chetan Mahajan wrote:
> > > > >
> > > > >> Thanks, Justin and Roland. While 2>/dev/null/ at the end of
> gmxdump
> > > > >> command
> > > > >> removes that quote nicely, adding either of following commands
> > fails.
> > > I
> > > > am
> > > > >> using gromacs 4.6.5.:
> > > > >>
> > > > >> Following did not work ( why? curious since above 2>/dev/null/
> will
> > > > >> suppress all errors getting displayed)
> > > > >>
> > > > >> 1. GMX_NO_QUOTES = 1
> > > > >> gmxdump -f lnanop.xtc
> > > > >>
> > > > >>
> > > > > Incorrect syntax.
> > > > >
> > > > > export GMX_NO_QUOTES=1
> > > > >
> > > > >
> > > > >  2. gmxdump -f lnanop.xtc -quiet
> > > > >>
> > > > >>
> > > > > The -quiet option will suppress quotes in 5.0, not 4.6.5, as Roland
> > > said.
> > > > >
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==
> > > > >
> > > > > Justin A. Lemkul, Ph.D.
> > > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > > >
> > > > > Department of Pharmaceutical Sciences
> > > > > School of Pharmacy
> > > > > Health Sciences Facility II, Room 601
> > > > > University of Maryland, Baltimore
> > > > > 20 Penn St.
> > > > > Baltimore, MD 21201
> > > > >
> > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > > > http://mackerell.umaryland.edu/~jalemkul
> > > > >
> > > > > ==
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https

Re: [gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Hi Justin,

If it's just gcq, then there is no problem to locate and remove. But as I
mentioned in one of the emails, there could be any other messages like "Thanx
for Using GROMACS - Have a Nice Day". So detecting them and manually
removing them does not seem smooth. I think 2 > stderr.log seems the best
option.

Thanks
Chetan


On Tue, Jul 8, 2014 at 11:47 AM, Justin Lemkul  wrote:

>
>
> On 7/8/14, 12:44 PM, Chetan Mahajan wrote:
>
>> Hi Tsjerk,
>>
>> Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end of
>> the command seems the only way out, since, as I said, I am also getting
>> greeting messages in addition to gcq quotes. However, adding  2>/dev/null
>>  will
>> also suppress unusual errors, if any at all. There does not seem a way out
>> of this.
>>
>>
> Is there a reason these quotes or messages are causing a problem?  If
> you're simply dumping to a text file, a simple grep -v "gcq" will get rid
> of the quotes lines and you can continue doing whatever you were doing
> before.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Thanks, Tsjerk and Justin. I was under the impression that there could be
non-gcq messages other than the one containing thanks. So I thought 2 >
stderr.log is the best option.


On Tue, Jul 8, 2014 at 3:50 PM, Tsjerk Wassenaar  wrote:

> Or:
>
> sed -i '/gcq/d;/Thanx/d;' dump.out
>
> on Mac:
>
> sed -i.bck '/gcq/d;/Thanx/d;' dump.out
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Jul 8, 2014 at 10:43 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/8/14, 4:02 PM, Chetan Mahajan wrote:
> >
> >> Hi Justin,
> >>
> >> If it's just gcq, then there is no problem to locate and remove. But as
> I
> >> mentioned in one of the emails, there could be any other messages like
> >> "Thanx
> >> for Using GROMACS - Have a Nice Day". So detecting them and manually
> >> removing them does not seem smooth. I think 2 > stderr.log seems the
> best
> >> option.
> >>
> >>
> > The "Thanx" message only shows up if you've disabled cool quotes, but
> > regardless this is another simple grep -v statement.
> >
> > grep -v "gcq" dump.out | grep -v "Thanx" > dump_clean.out
> >
> > would take care of both, regardless of cool quotes settings.
> >
> > -Justin
> >
> >
> >  Thanks
> >> Chetan
> >>
> >>
> >> On Tue, Jul 8, 2014 at 11:47 AM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 7/8/14, 12:44 PM, Chetan Mahajan wrote:
> >>>
> >>>  Hi Tsjerk,
> >>>>
> >>>> Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end
> of
> >>>> the command seems the only way out, since, as I said, I am also
> getting
> >>>> greeting messages in addition to gcq quotes. However, adding
> >>>>  2>/dev/null
> >>>>   will
> >>>> also suppress unusual errors, if any at all. There does not seem a way
> >>>> out
> >>>> of this.
> >>>>
> >>>>
> >>>>  Is there a reason these quotes or messages are causing a problem?  If
> >>> you're simply dumping to a text file, a simple grep -v "gcq" will get
> rid
> >>> of the quotes lines and you can continue doing whatever you were doing
> >>> before.
> >>>
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 601
> >>> University of Maryland, Baltimore
> >>> 20 Penn St.
> >>> Baltimore, MD 21201
> >>>
> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/
> >>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>>
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
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[gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

Hello Everyone,

ambconv.tgz (
http://www.gromacs.org/Downloads/User_contributions/Other_software)  tool
exists for converting Amer input files into the ones for Gromacs. Now, it's
README-eng file says that two Amber input files ( .atop (topology)  and
.rst (coordinates) ) are needed to generate input files for Gromacs.
Corresponding file formats in current Amber version are .prmtop and .inpcrd
respectively. Are these formats, just like older ones, exactly compatible
with this tool? If not, are there other tools to convert Amber input files
into the ones for Gromacs?

If this tool can be used, is the condition of removing all water before
applying this tool mandatory?

Thank you.

regards
Chetan
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

THis looks interesting, However, any version is giving following error on
test mentioned in README:

../acpype.py -i FFF.pdb
  File "../acpype.py", line 1231
with open(pklFile, "wb") as f:  # for python 2.6 or higher
^
SyntaxError: invalid syntax

Unfortunately, I do not know python.

Thanks
Chetan


On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. wrote:

> On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
> > are there other tools to convert Amber input files
> > into the ones for Gromacs?
>
> I've had success with acpype:
> https://code.google.com/p/acpype/
>
> Use the "amb2gmx" mode:
>
> acpype -p _prmtop_ -x _inpcrd_
>
> --
> Wes Barnett | jbarn...@tulane.edu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

THis looks interesting, However, any version is giving following error on
test mentioned in README:

../acpype.py -i FFF.pdb
  File "../acpype.py", line 1231
with open(pklFile, "wb") as f:  # for python 2.6 or higher
^
SyntaxError: invalid syntax

Unfortunately, I do not know python.

Thanks


On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. wrote:

> On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
> > are there other tools to convert Amber input files
> > into the ones for Gromacs?
>
> I've had success with acpype:
> https://code.google.com/p/acpype/
>
> Use the "amb2gmx" mode:
>
> acpype -p _prmtop_ -x _inpcrd_
>
> --
> Wes Barnett | jbarn...@tulane.edu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

I did play around lines 1231 and 1232, by keeping 1232, while removing
1231, etc etc. No success so far!


On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan  wrote:

> THis looks interesting, However, any version is giving following error on
> test mentioned in README:
>
> ../acpype.py -i FFF.pdb
>   File "../acpype.py", line 1231
> with open(pklFile, "wb") as f:  # for python 2.6 or higher
> ^
> SyntaxError: invalid syntax
>
> Unfortunately, I do not know python.
>
> Thanks
>
>
> On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. wrote:
>
>> On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
>> > are there other tools to convert Amber input files
>> > into the ones for Gromacs?
>>
>> I've had success with acpype:
>> https://code.google.com/p/acpype/
>>
>> Use the "amb2gmx" mode:
>>
>> acpype -p _prmtop_ -x _inpcrd_
>>
>> --
>> Wes Barnett | jbarn...@tulane.edu
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

Thanks, James. I already have python 2.4.
regards
Chetan


On Tue, Dec 3, 2013 at 8:45 PM, Barnett, James W. wrote:

> You shouldn't change any of the code unless you know what you're doing. If
> you remove lines it will not work as intended.
>
> I think you simply need to upgrade your version of Python 2, according to
> the error message.
>
> jbarn...@tulane.edu | from mobile
>
> Chetan Mahajan  wrote:
>
> >I did play around lines 1231 and 1232, by keeping 1232, while removing
> >1231, etc etc. No success so far!
> >
> >
> >On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan 
> wrote:
> >
> >> THis looks interesting, However, any version is giving following error
> on
> >> test mentioned in README:
> >>
> >> ../acpype.py -i FFF.pdb
> >>   File "../acpype.py", line 1231
> >> with open(pklFile, "wb") as f:  # for python 2.6 or higher
> >> ^
> >> SyntaxError: invalid syntax
> >>
> >> Unfortunately, I do not know python.
> >>
> >> Thanks
> >>
> >>
> >> On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W.  >wrote:
> >>
> >>> On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
> >>> > are there other tools to convert Amber input files
> >>> > into the ones for Gromacs?
> >>>
> >>> I've had success with acpype:
> >>> https://code.google.com/p/acpype/
> >>>
> >>> Use the "amb2gmx" mode:
> >>>
> >>> acpype -p _prmtop_ -x _inpcrd_
> >>>
> >>> --
> >>> Wes Barnett | jbarn...@tulane.edu
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>
> >>
>
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Re: [gmx-users] Amber to Gromacs conversion

[Chetan Mahajan]

This tool seems to be working. No errors so far.
Thanks
Chetan


On Tue, Dec 3, 2013 at 9:32 PM, Barnett, James W. wrote:

> Right, but according to the error message you need at least Python 2.6.
>
> jbarn...@tulane.edu | from mobile
>
> Chetan Mahajan  wrote:
>
> >Thanks, James. I already have python 2.4.
> >regards
> >Chetan
> >
> >
> >On Tue, Dec 3, 2013 at 8:45 PM, Barnett, James W.  >wrote:
> >
> >> You shouldn't change any of the code unless you know what you're doing.
> If
> >> you remove lines it will not work as intended.
> >>
> >> I think you simply need to upgrade your version of Python 2, according
> to
> >> the error message.
> >>
> >> jbarn...@tulane.edu | from mobile
> >>
> >> Chetan Mahajan  wrote:
> >>
> >> >I did play around lines 1231 and 1232, by keeping 1232, while removing
> >> >1231, etc etc. No success so far!
> >> >
> >> >
> >> >On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan 
> >> wrote:
> >> >
> >> >> THis looks interesting, However, any version is giving following
> error
> >> on
> >> >> test mentioned in README:
> >> >>
> >> >> ../acpype.py -i FFF.pdb
> >> >>   File "../acpype.py", line 1231
> >> >>     with open(pklFile, "wb") as f:  # for python 2.6 or higher
> >> >> ^
> >> >> SyntaxError: invalid syntax
> >> >>
> >> >> Unfortunately, I do not know python.
> >> >>
> >> >> Thanks
> >> >>
> >> >>
> >> >> On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. <
> jbarn...@tulane.edu
> >> >wrote:
> >> >>
> >> >>> On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
> >> >>> > are there other tools to convert Amber input files
> >> >>> > into the ones for Gromacs?
> >> >>>
> >> >>> I've had success with acpype:
> >> >>> https://code.google.com/p/acpype/
> >> >>>
> >> >>> Use the "amb2gmx" mode:
> >> >>>
> >> >>> acpype -p _prmtop_ -x _inpcrd_
> >> >>>
> >> >>> --
> >> >>> Wes Barnett | jbarn...@tulane.edu
> >> >>> --
> >> >>> Gromacs Users mailing list
> >> >>>
> >> >>> * Please search the archive at
> >> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> >>> posting!
> >> >>>
> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >>>
> >> >>> * For (un)subscribe requests visit
> >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> >> >>> send a mail to gmx-users-requ...@gromacs.org.
> >> >>>
> >> >>
> >> >>
> >>
>
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[gmx-users] position restraints

[Chetan Mahajan]

Hi,

I am including position restraints as one of the directives under
[moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)).

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;i  j  k  l   func   phase kd  pn
  2164   2162   2161   2163  1   180.00   4.60240   2 ;  H- O-
C-O1

[ position restraints ]
; ai   funct   fcxfcyfcz
  1   1   418400.0   418400.0   418400.0
  2   1   418400.0   418400.0   418400.0


 HOwever, I am following error:

ERROR 1 [file lnanop3_6.top, line 2207]:
  Invalid directive position restraints

Any clues will be appreciated.

Thanks
Chetan.
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Re: [gmx-users] position restraints

[Chetan Mahajan]

Thanks for all the replies. Yes, missing underscore was the problem. It's
solved.
Thanks
Chetan


On Thu, Jan 2, 2014 at 2:48 PM,  wrote:

> Hi,
> It seems you are missing the underscore between position & restraints in
> the directive.
> Check your code again.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Chetan
> Mahajan
> Sent: Thursday, January 02, 2014 4:41 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] position restraints
>
> Hi,
>
> I am including position restraints as one of the directives under
> [moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)).
>
> [ dihedrals ] ; impropers
> ; treated as propers in GROMACS to use correct AMBER analytical function
> ;i  j  k  l   func   phase kd  pn
>   2164   2162   2161   2163  1   180.00   4.60240   2 ;  H- O-
> C-O1
>
> [ position restraints ]
> ; ai   funct   fcxfcyfcz
>   1   1   418400.0   418400.0   418400.0
>   2   1   418400.0   418400.0   418400.0
>
>
>  HOwever, I am following error:
>
> ERROR 1 [file lnanop3_6.top, line 2207]:
>   Invalid directive position restraints
>
> Any clues will be appreciated.
>
> Thanks
> Chetan.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] position restraints

[Chetan Mahajan]

Resending my previous email, since earlier one failed for curious reason...


On Thu, Jan 2, 2014 at 4:21 PM, Chetan Mahajan  wrote:

> Thanks for all the replies. Yes, missing underscore was the problem. It's
> solved.
> Thanks
> Chetan
>
>
> On Thu, Jan 2, 2014 at 2:48 PM,  wrote:
>
>> Hi,
>> It seems you are missing the underscore between position & restraints in
>> the directive.
>> Check your code again.
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Chetan
>> Mahajan
>> Sent: Thursday, January 02, 2014 4:41 AM
>> To: gmx-us...@gromacs.org
>> Subject: [gmx-users] position restraints
>>
>> Hi,
>>
>> I am including position restraints as one of the directives under
>> [moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)).
>>
>> [ dihedrals ] ; impropers
>> ; treated as propers in GROMACS to use correct AMBER analytical function
>> ;i  j  k  l   func   phase kd  pn
>>   2164   2162   2161   2163  1   180.00   4.60240   2 ;  H- O-
>> C-O1
>>
>> [ position restraints ]
>> ; ai   funct   fcxfcyfcz
>>   1   1   418400.0   418400.0   418400.0
>>   2   1   418400.0   418400.0   418400.0
>>
>>
>>  HOwever, I am following error:
>>
>> ERROR 1 [file lnanop3_6.top, line 2207]:
>>   Invalid directive position restraints
>>
>> Any clues will be appreciated.
>>
>> Thanks
>> Chetan.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] gmx user forum not accessible

[Chetan Mahajan]

Is following the only way to search within mailing list archive?

1. search in gromacs mailing list (
http://www.gromacs.org/Support/Mailing_Lists/Search) for required key words.
2. Then open the links, but add "gromacs.org_" prior to "gmx-users" in
every link manually.

Thanks
Chetan


On Sun, Jan 5, 2014 at 7:44 PM, Justin Lemkul  wrote:

>
>
> On 1/5/14, 8:01 PM, Christian Wagner wrote:
>
>> Hi All,
>>
>> After I logged in, I tried to access information (
>> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079219.html)
>> from the gmx users archive and get the following error:
>>
>> Not Found
>>
>> The requested URL /pipermail/gmx-users/2013-March/079219.html was not
>> found on this server.
>>
>> Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443
>>
>>
>>
>> Where did the information get migrated to?
>>
>>
> Since some changes to the mailing list server, the URLs are different.
>  The lists.gromacs.org address correctly redirects to the new site, but
> you need to prefix "gmx-users" (or "gmx-developers") with "gromacs.org_",
> so your URL becomes:
>
> http://lists.gromacs.org/pipermail/gromacs.org_gmx-
> users/2013-March/079219.html
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] gmx user forum not accessible

[Chetan Mahajan]

Hi Rossen

Thanks. Just mentioning for overall benefit: Link provided in your email
does not work, although I can access nable forums at
http://gromacs.5086.x6.nabble.com/GROMACS-Users-Forum-f4370410.html.

Thanks
Chetan


On Thu, Jan 9, 2014 at 5:42 PM, Rossen Apostolov  wrote:

> Hi,
>
> This search page is deprecated (I just removed it). For searching use the
> integrated nable forums at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List.
>
> Same for the gmx-developers.
>
> Cheers,
> Rossen
>
>
> On 09/01/14 23:10, Chetan Mahajan wrote:
>
>> Is following the only way to search within mailing list archive?
>>
>> 1. search in gromacs mailing list (
>> http://www.gromacs.org/Support/Mailing_Lists/Search) for required key
>> words.
>> 2. Then open the links, but add "gromacs.org_" prior to "gmx-users" in
>> every link manually.
>>
>> Thanks
>> Chetan
>>
>>
>> On Sun, Jan 5, 2014 at 7:44 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/5/14, 8:01 PM, Christian Wagner wrote:
>>>
>>>  Hi All,
>>>>
>>>> After I logged in, I tried to access information (
>>>> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079219.html)
>>>> from the gmx users archive and get the following error:
>>>>
>>>> Not Found
>>>>
>>>> The requested URL /pipermail/gmx-users/2013-March/079219.html was not
>>>> found on this server.
>>>>
>>>> Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443
>>>>
>>>>
>>>>
>>>> Where did the information get migrated to?
>>>>
>>>>
>>>>  Since some changes to the mailing list server, the URLs are different.
>>>   The lists.gromacs.org address correctly redirects to the new site, but
>>> you need to prefix "gmx-users" (or "gmx-developers") with "gromacs.org_",
>>> so your URL becomes:
>>>
>>> http://lists.gromacs.org/pipermail/gromacs.org_gmx-
>>> users/2013-March/079219.html
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
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>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
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[gmx-users] error using pme option

[Chetan Mahajan]

Hi Everyone,

I am new to Gromacs and currently facing following error when I use pme
coulombtype in my energy minimization run.

Reading file lnanop.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI processes

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
*mdrun_mpi: symbol lookup error:
/home/cmahajan/program/gmx_intel64/bin/../lib/libmd_mpi.so.8: undefined
symbol: DftiCreateDescriptor_s_1d*
(same for other MPI processes)

Is it that "pme" coulombtype requires libraries which are not in the path?
Please advise how to go forward.

Files (mdp and run) that I use are as follows.

1. mdp file:

; VARIOUS PREPROCESSING OPTIONS =
;It gave message earlier wthen following was not commented out. Message was
"ignoring obselete mdp entry 'title' "
;title = Energy minimization of ligand_nanop-anatase-tio2

; Define can be used to control processes
define = -DFlEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 10.0
nsteps = 500 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type = grid ; Method to determine neighbor list (simple, grid)
*coulombtype = pme ; Treatment of long range electrostatic interactions*
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)

2. run file:


#PBS -S /bin/bash
#PBS -l nodes=1:ppn=4
#PBS -N energy_min3_18
#PBS -V

#!/bin/bash

LD_LIBRARY_PATH=/home/cmahajan/intel64
export LD_LIBRARY_PATH

# Set some environment variables
export PATH=/home/cmahajan/program/gmx_intel64/bin:$PATH
begin3=/home/cmahajan/work/begin-3

cd $begin3

#Energy minimization

mkdir 3_18
cd 3_18

mkdir min
cd min

grompp_mpi -f $begin3/min_lnanop3_18.mdp -c $begin3/lnanop.gro -p
$begin3/lnanop3_7.top -o lnanop.tpr

../../../../../../usr/local/bin/mpiexec -n 4  mdrun_mpi -deffnm lnanop

Thanks
Chetan
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[gmx-users] gdist: command not found

[Chetan Mahajan]

Hi,

I am trying to run gdist command on supercomputing system Stampede. Even
though I enter full path to Gromacs installed, it gives error--gdist:
command not found. Could you tell me the real issue here?

export PATH=/opt/apps/intel13/mvapich2_1_9/gromacs/4.6.3/bin:$PATH

gdist -f lnanop.xtc -s lnanop.tpr -n index.ndx

Upon running above I get:

gdist: command not found

Thanks
Chetan
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[gmx-users] center of mass

[Chetan Mahajan]

Hi,

Is there any analysis utility (g_?) that can calculate center of mass of
the group as a function of time? or plot a particular atom position as a
function of time?

Thanks in advance!

regards
Chetan
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[gmx-users] .top file after using amber2gromacs

[Chetan Mahajan]

Hi All

I have gromacs files generated using acpype tool acting on Amber files
originally.
I need to know the meaning of certain terms in that *.top file (email with
attachment of .top file got blocked due to attachment). Unfortunately, I
can't find on the web, any material regarding that. It would be great, if
anyone could comment on the following.

*1. What is the meaning of terms under defaults option at the top of the
file (pasted below)?*

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ   fudgeQQ
 12 yes  0.5
 0.8333

* 2a. ** Is atomtypes section needed? (sample .top file on gromacs website
does not have it) (pasted after 2b question)**In this atomtypes section,
the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a
simulation with these places zero be a valid simulation **?* My guess is
yes. THis is since, corresponding values are available later in atoms
section. The purpose of asking this question is that I have to be sure of
the runs I have made, that nothing has gone wrong in having those zeros.

* 2b.I see several enigmatic terms such as bond type p type, Amb. Can you
explain these terms, if they are necessary at all? Why last two columns for
Amb?*

(part of the data for both 2a and 2b pasted below)
[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon
Amb
 Ti   Ti  0.0  0.0   A 1.39461e-01
6.08772e-02 ; 0.78  0.0145
OT   OT   0.0  0.0   A 2.87832e-01
8.29687e-02 ; 1.62  0.0198
HW   HW  0.0  0.0   A 0.0e+00   0.0e+00
; 0.00  0.

*4.WHat is cgnr? how is it different from nr? (it appears in atoms section,
example below)*

 nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
 1   Ti 1   iO2TI1 1.691002 47.86700 ; qtot 1.691

Thanks
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Re: [gmx-users] .top file after using amber2gromacs

[Chetan Mahajan]

Hi All,

I would like to add to following question that simulation has so far been
physically ok. Thus, mostly having those zeroes there may not have
mattered, since later sections in the same .top file have masses and
charges specified.

Thanks
Chetan


On Sun, Mar 2, 2014 at 10:24 PM, Chetan Mahajan wrote:

> Hi All
>
> I have gromacs files generated using acpype tool acting on Amber files
> originally.
> I need to know the meaning of certain terms in that *.top file (email with
> attachment of .top file got blocked due to attachment). Unfortunately, I
> can't find on the web, any material regarding that. It would be great, if
> anyone could comment on the following.
>
> *1. What is the meaning of terms under defaults option at the top of the
> file (pasted below)?*
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ   fudgeQQ
>  12 yes  0.5
>  0.8333
>
> * 2a. ** Is atomtypes section needed? (sample .top file on gromacs
> website does not have it) (pasted after 2b question)**In this atomtypes
> section, the Amber2gromacs tool keeps mass and charge of each atom as zero.
> Would a simulation with these places zero be a valid simulation **?* My
> guess is yes. THis is since, corresponding values are available later in
> atoms section. The purpose of asking this question is that I have to be
> sure of the runs I have made, that nothing has gone wrong in having those
> zeros.
>
> * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you
> explain these terms, if they are necessary at all? Why last two columns for
> Amb?*
>
> (part of the data for both 2a and 2b pasted below)
> [ atomtypes ]
> ;name   bond_type mass charge   ptype   sigma epsilon
>   Amb
>  Ti   Ti  0.0  0.0   A 1.39461e-01
> 6.08772e-02 ; 0.78  0.0145
> OT   OT   0.0  0.0   A 2.87832e-01
> 8.29687e-02 ; 1.62  0.0198
> HW   HW  0.0  0.0   A 0.0e+00
> 0.0e+00 ; 0.00  0.
>
> *4.WHat is cgnr? how is it different from nr? (it appears in atoms
> section, example below)*
>
>  nr  type  resi  res  atom  cgnr charge  mass   ; qtot
> bond_type
>  1   Ti 1   iO2TI1 1.691002 47.86700 ; qtot 1.691
>
> Thanks
>
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Re: [gmx-users] .top file after using amber2gromacs

[Chetan Mahajan]

Thank you, Justin. Could you also tell me if atomtypes section is needed at
all? (sample .top file on gromacs website
does not have it).
regards
Chetan


On Sun, Mar 2, 2014 at 10:32 PM, Justin Lemkul  wrote:

>
>
> On 3/2/14, 11:24 PM, Chetan Mahajan wrote:
>
>> Hi All
>>
>> I have gromacs files generated using acpype tool acting on Amber files
>> originally.
>> I need to know the meaning of certain terms in that *.top file (email with
>> attachment of .top file got blocked due to attachment). Unfortunately, I
>> can't find on the web, any material regarding that. It would be great, if
>> anyone could comment on the following.
>>
>> *1. What is the meaning of terms under defaults option at the top of the
>> file (pasted below)?*
>>
>>
>> [ defaults ]
>> ; nbfunccomb-rule   gen-pairs   fudgeLJ   fudgeQQ
>>   12 yes  0.5
>>   0.8333
>>
>>
> Please refer to manual section 5.7.1, where each of these terms is
> explained after the urea.top example.
>
>  * 2a. ** Is atomtypes section needed? (sample .top file on gromacs website
>> does not have it) (pasted after 2b question)**In this atomtypes section,
>>
>> the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a
>> simulation with these places zero be a valid simulation **?* My guess is
>>
>> yes. THis is since, corresponding values are available later in atoms
>> section. The purpose of asking this question is that I have to be sure of
>> the runs I have made, that nothing has gone wrong in having those zeros.
>>
>>
> Charge and mass information in [atomtypes] is indeed over-written by
> whatever is found in [atoms].  You can always confirm what has been used by
> obtaining the grompp-processed topology with grompp -pp or by using gmxdump
> on the .tpr file.
>
>  * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you
>>
>> explain these terms, if they are necessary at all? Why last two columns
>> for
>> Amb?*
>>
>>
> Different force fields work in different ways, so the Gromacs file format
> is standard across all the different force fields.  Since there are
> generally fewer types of bonded interactions, bonded types are a subset of
> nonbonded types. Sometimes there are no differences, as is the case here.
>  If a force field uses separate bonded and nonbonded types, that just means
> the bonded types are an interpretation of the atom types used within
> ffbonded.itp.  The ptype column is particle type - A for atoms, S for
> shells, V for virtual sites.  The last two columns are a comment, likely
> the original AMBER parameters so you can verify the unit conversion.
>
>  (part of the data for both 2a and 2b pasted below)
>> [ atomtypes ]
>> ;name   bond_type mass charge   ptype   sigma epsilon
>> Amb
>>   Ti   Ti  0.0  0.0   A 1.39461e-01
>> 6.08772e-02 ; 0.78  0.0145
>>  OT   OT   0.0  0.0   A 2.87832e-01
>> 8.29687e-02 ; 1.62  0.0198
>>  HW   HW  0.0  0.0   A 0.0e+00
>> 0.0e+00
>> ; 0.00  0.
>>
>> *4.WHat is cgnr? how is it different from nr? (it appears in atoms
>> section,
>> example below)*
>>
>>
> cgnr = charge group number
> nr = atom number
>
> -Justin
>
>
>nr  type  resi  res  atom  cgnr charge  mass   ; qtot
>> bond_type
>>   1   Ti 1   iO2TI1 1.691002 47.86700 ; qtot 1.691
>>
>> Thanks
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] inclusion of water in gromacs input files

[Chetan Mahajan]

Hi,

I am new to gromacs and I used acpype (amber2gromacs) tool to generate
*.top and *.gro from Amber files *.prmtop and *.inpcrd. For  water, this
tool placed following in *.top file:


[ moleculetype ]
; molname   nrexcl ; TIP3P model
  WAT 2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1 OW  1 WAT O  1 -0.834   16.0
 2 HW  1 WATH1  1  0.4171.00800
 3 HW  1 WATH2  1  0.4171.00800

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572   462750.4
1   3   1   0.09572   462750.4

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.520836.800
#else
[ settles ]
; i   funct   length-oh length -hh
1   1   0.09572 0.15139

[ exclusions ]
1   2   3
2   1   3
3   1   2
#endif

[ system ]
 tio2_wpep

[ molecules ]
; Compoundnmols
 tio2_wpep1
 NA+  1
 WAT  3656

*My
question is it does not include any topology details for 3656 water
molecules either in this file or separately. Instead it has topology
defined for standard water molecule in atoms section above. However,
Gromacs accepted these two files as they are and runs were made. Please
comment if I need to include water topology details for all 3656 water
molecules. *

Thanks
Chetan
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[gmx-users] charge group number

[Chetan Mahajan]

Hi All

I am just learning how to assign charge group number. For TiO2 slab,
 amber2gromacs tool (acpype) I used assigns cgnr increasing consecutively
from Ti atoms followed by oxygen atoms. Clearly charge group here ( either
Ti or O) does not have zero charge. Can anyone throw light on why cgnr
should be like this (individual atoms) here?

Also in formate anion, should I have charge groups (charge in the bracket)
as
follows:

charge group 1 : C (0.9) and O (-0.88) together
charge group 2 : O (-0.88)
charge group 3: H (-0.147)

Thanks in advance,

regards
Chetan
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Re: [gmx-users] inclusion of water in gromacs input files

[Chetan Mahajan]

Thanks, Justin. By additional topology details, I meant bond and angle
topology information for each of the water molecules. I have used LAMMPS
before and it is needed there. So  it is not needed here, in Gromacs.

On Wednesday, March 5, 2014, Justin Lemkul  wrote:

>
>
> On 3/5/14, 1:42 AM, Chetan Mahajan wrote:
>
>> Hi,
>>
>> I am new to gromacs and I used acpype (amber2gromacs) tool to generate
>> *.top and *.gro from Amber files *.prmtop and *.inpcrd. For  water, this
>> tool placed following in *.top file:
>>
>>
>> [ moleculetype ]
>> ; molname   nrexcl ; TIP3P model
>>WAT 2
>>
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr charge   mass
>>   1 OW  1 WAT O  1 -0.834   16.0
>>   2 HW  1 WATH1  1  0.4171.00800
>>   3 HW  1 WATH2  1  0.4171.00800
>>
>> #ifdef FLEXIBLE
>> [ bonds ]
>> ; i j   funct   length  force.c.
>> 1   2   1   0.09572   462750.4
>> 1   3   1   0.09572   462750.4
>>
>> [ angles ]
>> ; i j   k   funct   angle   force.c.
>> 2   1   3   1   104.520836.800
>> #else
>> [ settles ]
>> ; i   funct   length-oh length -hh
>> 1   1   0.09572 0.15139
>>
>> [ exclusions ]
>> 1   2   3
>> 2   1   3
>> 3   1   2
>> #endif
>>
>> [ system ]
>>   tio2_wpep
>>
>> [ molecules ]
>> ; Compoundnmols
>>   tio2_wpep1
>>   NA+  1
>>   WAT  3656
>>
>>
>>  *My
>> question is it does not include any topology details for 3656 water
>> molecules either in this file or separately. Instead it has topology
>> defined for standard water molecule in atoms section above. However,
>> Gromacs accepted these two files as they are and runs were made. Please
>> comment if I need to include water topology details for all 3656 water
>> molecules. *
>>
>>
> What topology details would you include?  The program simply printed a
> full TIP3P topology, which mimics the effect of #including the tip3p.itp
> file.  It is a complete water topology and needs nothing else.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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[gmx-users] sigma unit conversion

[Chetan Mahajan]

Hi all,

I am using Amber2gromacs tool called as acpype for converting input files
to Amber to input files for gromacs. I have a question regarding atomtypes
section of .top file. Here are first two rows of that section in my file:

name   bond_type mass charge   ptype   sigma epsilon
 Amb
 Ti   Ti0.0  0.0A 1.39461e-01
6.08772e-02 ; 0.78  0.0145
 OT   OT0.0  0.0A 2.87832e-01   8.29687e-02
; 1.62  0.0198

Now, in my .top file, each row contains, at the end, Amber force field
values for sigma and epsilon are given. Values on the left indicate unit
converted values. However, given that Amber units are A0 for sigma,
converted value for gromacs, which should be in nanometer does not match.
Combination rule chosen is 2. ( by the way, how is this rule chosen ?)

Thanks
Chetan
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[gmx-users] impropers in Gromacs and acepype tool

[Chetan Mahajan]

Hi

I just wanted to check the order of atoms in a improper in gromacs input
file *.top. According to urea example on page 137 ( section 5.7)of manual
4.6.4, order of i,j,k,l atoms in improper always starts with central atom,
whereas that in a *.top file generated with acepype lists i,j,k,l order for
improper in formate ion as H O C O. Central atom at third position. Is this
right or bug in the tool acepype?

I appreciate your response.

Thanks
Chetan
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Re: [gmx-users] impropers in Gromacs and acepype tool

[Chetan Mahajan]

Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have just
one .top file which contains topologies and parameters. Just curious: where
to get Amber parameter set from?


On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul  wrote:

>
>
> On 3/6/14, 5:16 PM, Chetan Mahajan wrote:
>
>> Hi
>>
>> I just wanted to check the order of atoms in a improper in gromacs input
>> file *.top. According to urea example on page 137 ( section 5.7)of manual
>> 4.6.4, order of i,j,k,l atoms in improper always starts with central atom,
>> whereas that in a *.top file generated with acepype lists i,j,k,l order
>> for
>> improper in formate ion as H O C O. Central atom at third position. Is
>> this
>> right or bug in the tool acepype?
>>
>>
> It's right.  The example in the manual is for Gromos force fields.  You
> should look at the actual .rtp files for the AMBER parameter set you're
> trying to use.  Suffice it to say that different atom orders are supported,
> because the Gromacs machinery (specifically pdb2gmx) knows how to deal with
> lots of stuff based on bonded geometry.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] impropers in Gromacs and acepype tool

[Chetan Mahajan]

I think acepype Amber2gromacs tool has amber parameter files. but here is
no .rtp


On Thu, Mar 6, 2014 at 4:40 PM, Chetan Mahajan  wrote:

> Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have
> just one .top file which contains topologies and parameters. Just curious:
> where to get Amber parameter set from?
>
>
> On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 3/6/14, 5:16 PM, Chetan Mahajan wrote:
>>
>>> Hi
>>>
>>> I just wanted to check the order of atoms in a improper in gromacs input
>>> file *.top. According to urea example on page 137 ( section 5.7)of manual
>>> 4.6.4, order of i,j,k,l atoms in improper always starts with central
>>> atom,
>>> whereas that in a *.top file generated with acepype lists i,j,k,l order
>>> for
>>> improper in formate ion as H O C O. Central atom at third position. Is
>>> this
>>> right or bug in the tool acepype?
>>>
>>>
>> It's right.  The example in the manual is for Gromos force fields.  You
>> should look at the actual .rtp files for the AMBER parameter set you're
>> trying to use.  Suffice it to say that different atom orders are supported,
>> because the Gromacs machinery (specifically pdb2gmx) knows how to deal with
>> lots of stuff based on bonded geometry.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>>
>
>
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[gmx-users] tip3p

[Chetan Mahajan]

Hi All

I have tip3p water potential parameters from 3 different sources and they
differ quite substantially. I tried finding answer on the web or manual,
but no success.
Following lists all the three sources and bond potential force constant
(kb) value, in bracket as an example of how values differ in all the three
sources.

1. From the article: Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys.
1996, 105, 1902. (kb= 450 kcal/(mol.A02)), where A0 is angstrom. ( in
Gromacs units,
kb=188280 kcal/(mol.A02))

2. From tip3p files in forcefield directories in
gromacs/4.6.3/share/gromacs/top
(502416.0 kJ/(mol.nm2)

3. That used by acpype tool while converting amber input files to gromacs
input files.( 462750.4 kJ/(mol.nm2))

2 and 3 force constant units should conform to Gromacs, so kJ and nm.

It's very confusing, surprising and disappointing why these three values
differ so much. What is the correct value and why? I really appreciate your
response.

Thanks
Chetan
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Re: [gmx-users] tip3p

[Chetan Mahajan]

Hi Mark,

Thanks for the reply. Now, 1983 article by Jorgensen gives parameters for
rigid tip3p, whereas I am seeking that for flexible tip3p. Force constant
is not mentioned in 1983 article by Jorgensen. The article that I cited in
#1 point below gives these parameters for modified tip3p. I do not
understand why these are different from those in tip3p files in gromacs
installed. Is there any other article describing flexible tip3p parameters?

Thanks
Chetan


On Sun, Mar 9, 2014 at 7:33 AM, Mark Abraham wrote:

> On Sun, Mar 9, 2014 at 1:00 PM, Chetan Mahajan 
> wrote:
>
> > Hi All
> >
> > I have tip3p water potential parameters from 3 different sources and they
> > differ quite substantially. I tried finding answer on the web or manual,
> > but no success.
> > Following lists all the three sources and bond potential force constant
> > (kb) value, in bracket as an example of how values differ in all the
> three
> > sources.
> >
> > 1. From the article: Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys.
> > 1996, 105, 1902. (kb= 450 kcal/(mol.A02)), where A0 is angstrom. ( in
> > Gromacs units,
> > kb=188280 kcal/(mol.A02))
> >
>
> This is not the TIP3P citation (see gromacs manual), and as you can see in
> the penultimate paragraph, it does not even use the standard TIP3P.
>
> 2. From tip3p files in forcefield directories in
> > gromacs/4.6.3/share/gromacs/top
> > (502416.0 kJ/(mol.nm2)
> >
>
> This agrees with Jorgensen 1983
>
>
> > 3. That used by acpype tool while converting amber input files to gromacs
> > input files.( 462750.4 kJ/(mol.nm2))
> >
>
> No idea where this is from or what it is doing, but presumably reading the
> documentation or code will be a good start! :-)
>
> Mark
>
>
> > 2 and 3 force constant units should conform to Gromacs, so kJ and nm.
> >
> > It's very confusing, surprising and disappointing why these three values
> > differ so much. What is the correct value and why? I really appreciate
> your
> > response.
> >
> > Thanks
> > Chetan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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[gmx-users] surprising: what's the reason?

[Chetan Mahajan]

Hi

I am testing one MD run using gromacs. 2 days back it ran fine. Today when
I ran the "exactly same" code again, it gave following error:


Increasing the number of cell to communicate in dimension X to 3 for the
first time

---
Program mdrun_mpi, VERSION 4.6.3
Source code file:
/admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c, line:
2730

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

I am confused as to why same run should give different answers on different
occasions. Is it pointing to something wrong with the gromacs executable I
have or something else?

Thank you.

regards
Chetan
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Re: [gmx-users] surprising: what's the reason?

[Chetan Mahajan]

Hi Tsjerk,

Thanks. It is on the same machine Stampede, same number of nodes and
processors. It does go through minimization part (5000 steps) well and
gives this error near the start of equilibration run, which comes after
minimization.

Thank you.

regards
Chetan


On Wed, Mar 12, 2014 at 12:50 AM, Tsjerk Wassenaar wrote:

> Hi Chetan,
>
> Was it on the same machine/node(s)? Same number of processors? How many
> steps until the error? Any difference may cause a different outcome.
>
> Cheers,
>
> Tsjerk
> On Mar 12, 2014 5:42 AM, "Chetan Mahajan"  wrote:
>
> > Hi
> >
> > I am testing one MD run using gromacs. 2 days back it ran fine. Today
> when
> > I ran the "exactly same" code again, it gave following error:
> >
> >
> > Increasing the number of cell to communicate in dimension X to 3 for the
> > first time
> >
> > ---
> > Program mdrun_mpi, VERSION 4.6.3
> > Source code file:
> > /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c,
> line:
> > 2730
> >
> > Fatal error:
> > One of the box vectors has become shorter than twice the cut-off length
> or
> > box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> >
> > I am confused as to why same run should give different answers on
> different
> > occasions. Is it pointing to something wrong with the gromacs executable
> I
> > have or something else?
> >
> > Thank you.
> >
> > regards
> > Chetan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] surprising: what's the reason?

[Chetan Mahajan]

Hi Mark, Tsjerk and others interested,

I changed the frequency of nstxout, nstvout, nstlog, nstenergy, nstxtcout
in equilibration run from 1000 to 1 and Whoa! the entire code (even if the
frequency of these in production run is still 1000) is running fine now.
That box vector error is gone. I wonder what's going on, but I am happy
code is working. I have confirmed this by reproducing this run yet again.
 ( Code still gives box vector error when output frequency is 1000 instead
of 1 ).

Thanks
Chetan


On Wed, Mar 12, 2014 at 4:20 AM, Mark Abraham wrote:

> Sounds like a normal case of being too rough with a system during
> equilibration, which can lead to
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up if you get
> unlucky. There's general advice there.
>
> Mark
>
>
> On Wed, Mar 12, 2014 at 7:05 AM, Chetan Mahajan  >wrote:
>
> > Hi Tsjerk,
> >
> > Thanks. It is on the same machine Stampede, same number of nodes and
> > processors. It does go through minimization part (5000 steps) well and
> > gives this error near the start of equilibration run, which comes after
> > minimization.
> >
> > Thank you.
> >
> > regards
> > Chetan
> >
> >
> > On Wed, Mar 12, 2014 at 12:50 AM, Tsjerk Wassenaar  > >wrote:
> >
> > > Hi Chetan,
> > >
> > > Was it on the same machine/node(s)? Same number of processors? How many
> > > steps until the error? Any difference may cause a different outcome.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > > On Mar 12, 2014 5:42 AM, "Chetan Mahajan" 
> wrote:
> > >
> > > > Hi
> > > >
> > > > I am testing one MD run using gromacs. 2 days back it ran fine. Today
> > > when
> > > > I ran the "exactly same" code again, it gave following error:
> > > >
> > > >
> > > > Increasing the number of cell to communicate in dimension X to 3 for
> > the
> > > > first time
> > > >
> > > > ---
> > > > Program mdrun_mpi, VERSION 4.6.3
> > > > Source code file:
> > > > /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c,
> > > line:
> > > > 2730
> > > >
> > > > Fatal error:
> > > > One of the box vectors has become shorter than twice the cut-off
> length
> > > or
> > > > box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> > > >
> > > > I am confused as to why same run should give different answers on
> > > different
> > > > occasions. Is it pointing to something wrong with the gromacs
> > executable
> > > I
> > > > have or something else?
> > > >
> > > > Thank you.
> > > >
> > > > regards
> > > > Chetan
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
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> > > >
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Re: [gmx-users] surprising: what's the reason?

[Chetan Mahajan]

Hi Mark,

Could you clarify what is meant by "gentle" and why does it help solve the
issue?

Thanks
Chetan


On Sun, Mar 16, 2014 at 8:29 AM, Mark Abraham wrote:

> Ja. Rebuilding the neighbor list more often is more gentle, which often
> helps. The output period has nothing directly to do with it.
>
> Mark
> On Mar 16, 2014 8:18 AM, "Tsjerk Wassenaar"  wrote:
>
> > Hi Chetan,
> >
> > nstenergy = 1 requires nstcalcenergy = 1, which requires nstlist = 1. You
> > might want to try setting only the latter, and check nstpcoupl.
> >
> > Hope it helps ,
> >
> > Tsjerk
> > On Mar 16, 2014 7:17 AM, "Chetan Mahajan"  wrote:
> >
> > > Hi Mark, Tsjerk and others interested,
> > >
> > > I changed the frequency of nstxout, nstvout, nstlog, nstenergy,
> nstxtcout
> > > in equilibration run from 1000 to 1 and Whoa! the entire code (even if
> > the
> > > frequency of these in production run is still 1000) is running fine
> now.
> > > That box vector error is gone. I wonder what's going on, but I am happy
> > > code is working. I have confirmed this by reproducing this run yet
> again.
> > >  ( Code still gives box vector error when output frequency is 1000
> > instead
> > > of 1 ).
> > >
> > > Thanks
> > > Chetan
> > >
> > >
> > > On Wed, Mar 12, 2014 at 4:20 AM, Mark Abraham <
> mark.j.abra...@gmail.com
> > > >wrote:
> > >
> > > > Sounds like a normal case of being too rough with a system during
> > > > equilibration, which can lead to
> > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up if you
> get
> > > > unlucky. There's general advice there.
> > > >
> > > > Mark
> > > >
> > > >
> > > > On Wed, Mar 12, 2014 at 7:05 AM, Chetan Mahajan <
> chetanv...@gmail.com
> > > > >wrote:
> > > >
> > > > > Hi Tsjerk,
> > > > >
> > > > > Thanks. It is on the same machine Stampede, same number of nodes
> and
> > > > > processors. It does go through minimization part (5000 steps) well
> > and
> > > > > gives this error near the start of equilibration run, which comes
> > after
> > > > > minimization.
> > > > >
> > > > > Thank you.
> > > > >
> > > > > regards
> > > > > Chetan
> > > > >
> > > > >
> > > > > On Wed, Mar 12, 2014 at 12:50 AM, Tsjerk Wassenaar <
> > tsje...@gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Hi Chetan,
> > > > > >
> > > > > > Was it on the same machine/node(s)? Same number of processors?
> How
> > > many
> > > > > > steps until the error? Any difference may cause a different
> > outcome.
> > > > > >
> > > > > > Cheers,
> > > > > >
> > > > > > Tsjerk
> > > > > > On Mar 12, 2014 5:42 AM, "Chetan Mahajan" 
> > > > wrote:
> > > > > >
> > > > > > > Hi
> > > > > > >
> > > > > > > I am testing one MD run using gromacs. 2 days back it ran fine.
> > > Today
> > > > > > when
> > > > > > > I ran the "exactly same" code again, it gave following error:
> > > > > > >
> > > > > > >
> > > > > > > Increasing the number of cell to communicate in dimension X to
> 3
> > > for
> > > > > the
> > > > > > > first time
> > > > > > >
> > > > > > > ---
> > > > > > > Program mdrun_mpi, VERSION 4.6.3
> > > > > > > Source code file:
> > > > > > >
> > > /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c,
> > > > > > line:
> > > > > > > 2730
> > > > > > >
> > > > > > > Fatal error:
> > > > > > > One of the box vectors has become shorter than twice the
> cut-off
> > > > length
> > > > > > or
> > > > > > > box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> > > > > > >
> > > > > > > I am confus

Re: [gmx-users] surprising: what's the reason?

[Chetan Mahajan]

I am a bit perplexed at this data about the box vector error I mentioned in
first email:

  nstxout 1000 10 1 10 1000 1000 1000 1  nstvout 1000 10 1 10 1000 1000 1000
1  nstlog 1000 10 1 10 1000 1000 1000 1  nstenergy 1000 10 1 10 1000 1000
1000 10  nstxtcout 1000 10 1 10 1000 1000 1000 1  nstlist 10 10 1 1 1
5 2 10
error yes   yesno
 no noyes
nono

Columns represent values chosen in different runs for the options on
extreme left. Row at the bottom indicate if error occurred in that row. As
we see, for the runs for which nstlist was 1 or 2, no error was observed.
Now, when nstlist is 10 (column 2 and column 8), conflicting results were
obtained. From column 2 and 8, we observe that just making nstxout,
nstvout, nstlog, nstxtcout = 1, no error is observed. Why should error
depend on these options?

Thanks
Chetan

On Mon, Mar 17, 2014 at 1:22 AM, Chetan Mahajan wrote:

> Hi Mark,
>
> Could you clarify what is meant by "gentle" and why does it help solve the
> issue?
>
> Thanks
> Chetan
>
>
> On Sun, Mar 16, 2014 at 8:29 AM, Mark Abraham wrote:
>
>> Ja. Rebuilding the neighbor list more often is more gentle, which often
>> helps. The output period has nothing directly to do with it.
>>
>> Mark
>> On Mar 16, 2014 8:18 AM, "Tsjerk Wassenaar"  wrote:
>>
>> > Hi Chetan,
>> >
>> > nstenergy = 1 requires nstcalcenergy = 1, which requires nstlist = 1.
>> You
>> > might want to try setting only the latter, and check nstpcoupl.
>> >
>> > Hope it helps ,
>> >
>> > Tsjerk
>> > On Mar 16, 2014 7:17 AM, "Chetan Mahajan"  wrote:
>> >
>> > > Hi Mark, Tsjerk and others interested,
>> > >
>> > > I changed the frequency of nstxout, nstvout, nstlog, nstenergy,
>> nstxtcout
>> > > in equilibration run from 1000 to 1 and Whoa! the entire code (even if
>> > the
>> > > frequency of these in production run is still 1000) is running fine
>> now.
>> > > That box vector error is gone. I wonder what's going on, but I am
>> happy
>> > > code is working. I have confirmed this by reproducing this run yet
>> again.
>> > >  ( Code still gives box vector error when output frequency is 1000
>> > instead
>> > > of 1 ).
>> > >
>> > > Thanks
>> > > Chetan
>> > >
>> > >
>> > > On Wed, Mar 12, 2014 at 4:20 AM, Mark Abraham <
>> mark.j.abra...@gmail.com
>> > > >wrote:
>> > >
>> > > > Sounds like a normal case of being too rough with a system during
>> > > > equilibration, which can lead to
>> > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up if you
>> get
>> > > > unlucky. There's general advice there.
>> > > >
>> > > > Mark
>> > > >
>> > > >
>> > > > On Wed, Mar 12, 2014 at 7:05 AM, Chetan Mahajan <
>> chetanv...@gmail.com
>> > > > >wrote:
>> > > >
>> > > > > Hi Tsjerk,
>> > > > >
>> > > > > Thanks. It is on the same machine Stampede, same number of nodes
>> and
>> > > > > processors. It does go through minimization part (5000 steps) well
>> > and
>> > > > > gives this error near the start of equilibration run, which comes
>> > after
>> > > > > minimization.
>> > > > >
>> > > > > Thank you.
>> > > > >
>> > > > > regards
>> > > > > Chetan
>> > > > >
>> > > > >
>> > > > > On Wed, Mar 12, 2014 at 12:50 AM, Tsjerk Wassenaar <
>> > tsje...@gmail.com
>> > > > > >wrote:
>> > > > >
>> > > > > > Hi Chetan,
>> > > > > >
>> > > > > > Was it on the same machine/node(s)? Same number of processors?
>> How
>> > > many
>> > > > > > steps until the error? Any difference may cause a different
>> > outcome.
>> > > > > >
>> > > > > > Cheers,
>> > > > > >
>> > > > > > Tsjerk
>> > > > > > On Mar 12, 2014 5:42 AM, "Chetan Mahajan" > >
>> > > > wrote:
>> > > > > >
>> > > > > >

[gmx-users] refcoord-scaling

[Chetan Mahajan]

Dear all:

I am trying to get a simulation of water solvated titanium oxide running.
When 'all' option is used for refcoord-scaling, simulation runs ok.
However, when 'com' option is used for refcoord-scaling, simulation crashes
with any of the following errors. Could anyone explain to me why is this
happening or when each of the options such as 'all', 'com' and 'no' is used?

Thanks a lot!
regards
Chetan


Errors:

X particles communicated to PME node Y are more than a cell length out of
the domain decomposition cell of their charge group

This is another way that mdrun tells you your system is blowing
up.
In GROMACS version 4.0, domain decomposition was introduced to divide the
system into regions containing nearby atoms (for more details, see the
manual  or the GROMACS 4
paper).
If you have particles that are flying across the system, you will get this
fatal error. The message indicates that some piece of your system is
tearing apart (hence out of the "cell of their charge group"). Refer
to the Blowing
Up  page for
advice on how to fix this issue.


A charge group moved too far between two domain decomposition steps.
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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

When 4 times lower timestep is used, simulation runs a bit longer, but does
crash after that.


On Sun, Mar 23, 2014 at 7:05 PM, Chetan Mahajan wrote:

> Dear all:
>
> I am trying to get a simulation of water solvated titanium oxide running.
> When 'all' option is used for refcoord-scaling, simulation runs ok.
> However, when 'com' option is used for refcoord-scaling, simulation crashes
> with any of the following errors. Could anyone explain to me why is this
> happening or when each of the options such as 'all', 'com' and 'no' is used?
>
> Thanks a lot!
> regards
> Chetan
>
>
> Errors:
>
> X particles communicated to PME node Y are more than a cell length out of
> the domain decomposition cell of their charge group
>
> This is another way that mdrun tells you your system is blowing 
> up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> In GROMACS version 4.0, domain decomposition was introduced to divide the
> system into regions containing nearby atoms (for more details, see the
> manual <http://www.gromacs.org/Documentation/Manual> or the GROMACS 4
> paper <http://dx.doi.org/10.1021/ct700301q>). If you have particles that
> are flying across the system, you will get this fatal error. The message
> indicates that some piece of your system is tearing apart (hence out of the
> "cell of their charge group"). Refer to the Blowing 
> Up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up> page
> for advice on how to fix this issue.
>
>
> A charge group moved too far between two domain decomposition steps.
>
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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Hi Mark,

I am restraining positions of each of the atoms of TiO2 crystal. Could you
comment again why should simulation crash when 'com' option is used against
'all' option? Also, description in the manual does not answer my question:
when is 'all' option generally used? When is 'com' option generally used?
When is 'no' option generally used?

Thanks!

regards
Chetan


On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham wrote:

> On Mar 24, 2014 1:10 AM, "Chetan Mahajan"  wrote:
> >
> > Dear all:
> >
> > I am trying to get a simulation of water solvated titanium oxide running.
> > When 'all' option is used for refcoord-scaling, simulation runs ok.
> > However, when 'com' option is used for refcoord-scaling, simulation
> crashes
> > with any of the following errors. Could anyone explain to me why is this
> > happening
>
> See the description of com. You didn't tell us what you were restraining,
> so it's hard to help. But I can see multiple com of tio2 and PBC not
> working well together, particularly if you box size is far from best.
>
> > or when each of the options such as 'all', 'com' and 'no' is used?
>
> When you really care about your starting position and need to equilibrate
> in NPT.
>
> Mark
>
> > Thanks a lot!
> > regards
> > Chetan
> >
> >
> > Errors:
> >
> > X particles communicated to PME node Y are more than a cell length out of
> > the domain decomposition cell of their charge group
> >
> > This is another way that mdrun tells you your system is blowing
> > up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> > In GROMACS version 4.0, domain decomposition was introduced to divide the
> > system into regions containing nearby atoms (for more details, see the
> > manual <http://www.gromacs.org/Documentation/Manual> or the GROMACS 4
> > paper<http://dx.doi.org/10.1021/ct700301q>).
> > If you have particles that are flying across the system, you will get
> this
> > fatal error. The message indicates that some piece of your system is
> > tearing apart (hence out of the "cell of their charge group"). Refer
> > to the Blowing
> > Up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up> page
> for
> > advice on how to fix this issue.
> >
> >
> > A charge group moved too far between two domain decomposition steps.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Thanks, Mark. So is 'all' option okay when positions of each of the atoms
of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
does not seem correct, since positions of the atoms of TiO2 crystal change
when 'all' option is applied. However, it does not give error as 'com'
option does.

regards
Chetan


On Mon, Mar 24, 2014 at 11:16 AM, Mark Abraham wrote:

> On Mon, Mar 24, 2014 at 4:44 PM, Chetan Mahajan  >wrote:
>
> > Hi Mark,
> >
> > I am restraining positions of each of the atoms of TiO2 crystal. Could
> you
> > comment again why should simulation crash when 'com' option is used
> against
> > 'all' option?
>
>
> Don't know, I'd have to read the code, and I don't care enough to do that
> :-) But if you had a molecule whose COM might cross PBC while
> equilibrating, and the implementation had some limitation that was
> described with "only one COM is used, even when there are multiple
> molecules" then I'd be expecting problems.
>
>
> > Also, description in the manual does not answer my question:
> > when is 'all' option generally used? When is 'com' option generally used?
> > When is 'no' option generally used?
> >
>
> When they work for your case. But they are all hacks for doing something
> artificial, like getting a system equilibrated. When and why would depend
> on things like how many restrained sites per molecule, how rigid the model
> of the molecule  was..
>
> Mark
>
>
> >
> > Thanks!
> >
> > regards
> > Chetan
> >
> >
> > On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham  > >wrote:
> >
> > > On Mar 24, 2014 1:10 AM, "Chetan Mahajan" 
> wrote:
> > > >
> > > > Dear all:
> > > >
> > > > I am trying to get a simulation of water solvated titanium oxide
> > running.
> > > > When 'all' option is used for refcoord-scaling, simulation runs ok.
> > > > However, when 'com' option is used for refcoord-scaling, simulation
> > > crashes
> > > > with any of the following errors. Could anyone explain to me why is
> > this
> > > > happening
> > >
> > > See the description of com. You didn't tell us what you were
> restraining,
> > > so it's hard to help. But I can see multiple com of tio2 and PBC not
> > > working well together, particularly if you box size is far from best.
> > >
> > > > or when each of the options such as 'all', 'com' and 'no' is used?
> > >
> > > When you really care about your starting position and need to
> equilibrate
> > > in NPT.
> > >
> > > Mark
> > >
> > > > Thanks a lot!
> > > > regards
> > > > Chetan
> > > >
> > > >
> > > > Errors:
> > > >
> > > > X particles communicated to PME node Y are more than a cell length
> out
> > of
> > > > the domain decomposition cell of their charge group
> > > >
> > > > This is another way that mdrun tells you your system is blowing
> > > > up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> > > > In GROMACS version 4.0, domain decomposition was introduced to divide
> > the
> > > > system into regions containing nearby atoms (for more details, see
> the
> > > > manual <http://www.gromacs.org/Documentation/Manual> or the GROMACS
> 4
> > > > paper<http://dx.doi.org/10.1021/ct700301q>).
> > > > If you have particles that are flying across the system, you will get
> > > this
> > > > fatal error. The message indicates that some piece of your system is
> > > > tearing apart (hence out of the "cell of their charge group"). Refer
> > > > to the Blowing
> > > > Up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
> page
> > > for
> > > > advice on how to fix this issue.
> > > >
> > > >
> > > > A charge group moved too far between two domain decomposition steps.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > 

Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Hi Justin,

My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656
water molecules, 1 formate anion and 1 sodium ion.  Is it true that when
'all' option is used, positions of the atoms (meant to be restrained)
always change?

Thanks
Chetan


On Mon, Mar 24, 2014 at 7:37 PM, Justin Lemkul  wrote:

>
>
> On 3/24/14, 8:29 PM, Chetan Mahajan wrote:
>
>> Thanks, Mark. So is 'all' option okay when positions of each of the atoms
>> of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
>> does not seem correct, since positions of the atoms of TiO2 crystal change
>> when 'all' option is applied. However, it does not give error as 'com'
>> option does.
>>
>>
> Is your system just a TiO2 crystal?  Is there any solvent?  If it's just a
> crystal, I see no point in restraining anything.  It is very unusual that
> the "all" option of refcoord-scaling is more stable than "com" - normally
> the opposite is true.  But that also explains why the coordinates are
> changing - the reference position of each individual atom is scaled
> according to the pressure coupling matrix, so the atoms are restrained to a
> dynamic reference, so it seems that it's not really accomplishing anything.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Thanks, Justin. I am trying to understand what is meant by 'com' option.
Following two sentences in manual seem conflicting with each other:

"*Scale* the center of mass of the reference coordinates with the scaling
matrix of the pressure coupling. The *vectors of each reference
coordinate*to the center of mass are *not
scaled*."

Doesn't scaling center of mass of reference coordinates change something
else ? reference coordinates?

Thanks

Chetan


On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul  wrote:

>
>
> On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
>
>> Hi Justin,
>>
>> My system is TiO2 crystal (2160 atoms position restrained) solvated by
>> 3656
>> water molecules, 1 formate anion and 1 sodium ion.  Is it true that when
>> 'all' option is used, positions of the atoms (meant to be restrained)
>> always change?
>>
>>
> Consider what position restraints are doing.  They never guarantee that
> atoms won't move; they just apply a biasing potential to disfavor movement.
>  So yes, your atoms will probably move.  The smaller the system, the larger
> the effect will likely be.  Consider also what reference coordinates are
> doing.  They define how strong the potential is (distance between current
> coordinates and reference).  If you're scaling all atoms individually
> according to the pressure coupling, the reference moves and therefore the
> atoms can also move.  For larger systems like proteins, "refcoord_scaling =
> com" is normal and stable, and "refcoord_scaling = all" is disfavored.
>  Honestly, I don't know what to expect for a very small system like yours,
> but it is likely to be affected to a greater extent.
>
> If the "all" option gives you a stable simulation that allow for proper
> equilibration, then I doubt there is any real problem.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Hi,

Thanks a lot. It is clearer, but I have questions, so this email:

Why is option "none" not desirable, if we want to restrain positions of
atoms of crystal to specific points? Isn't the strain generated due to
atoms scaling but not reference coordinates helping? Why is none option
better than "com"? Is the possible movement of crystal due to "com" option
desirable?

If a particular option exists, then it does so for a particular purpose. In
which case, "none" or "all" be a valid option?

Thanks
Chetan


On Mon, Mar 24, 2014 at 10:40 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Say you have a box with an x-side length of 3 nm and two atoms with
> x-dimension position restraints to: (a) x=1 nm, and (b) x=2 nm
>
> Then let the box shrink to 99% of its previous size due to pressure
> coupling. The following is my understanding of  the locations to which the
> atoms will be restrained:
>
> refcoord_scaling =
>
> none:
> (a) x=1 nm, and (b) x=2 nm  -- note how the restraint positions are not
> scaled (even though the positions of the atoms are scaled due to pressure
> coupling)
>
> all:
> (a) x=0.99 nm, and (b) x=1.98 nm   -- note how the atoms are now
> restrained to be closer together
>
> com:
> (a) x=0.985 nm, and (b) x=1.985 nm  -- note how the distance between the
> atoms is maintained
>
>
> So you see how "none" leads to problems because the restraint reference
> positions are not scaled at all with the atomic positions and how "all"
> leads to problems because, if you restrained all Ca atoms, then you would
> get compression/expansion of the size of your protein as the system
> fluctuated in constant pressure simulations.
>
> Chris.
> ________
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Chetan
> Mahajan 
> Sent: 24 March 2014 23:25
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] refcoord-scaling
>
> Thanks, Justin. I am trying to understand what is meant by 'com' option.
> Following two sentences in manual seem conflicting with each other:
>
> "*Scale* the center of mass of the reference coordinates with the scaling
> matrix of the pressure coupling. The *vectors of each reference
> coordinate*to the center of mass are *not
> scaled*."
>
> Doesn't scaling center of mass of reference coordinates change something
> else ? reference coordinates?
>
> Thanks
>
> Chetan
>
>
> On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
> >
> >> Hi Justin,
> >>
> >> My system is TiO2 crystal (2160 atoms position restrained) solvated by
> >> 3656
> >> water molecules, 1 formate anion and 1 sodium ion.  Is it true that when
> >> 'all' option is used, positions of the atoms (meant to be restrained)
> >> always change?
> >>
> >>
> > Consider what position restraints are doing.  They never guarantee that
> > atoms won't move; they just apply a biasing potential to disfavor
> movement.
> >  So yes, your atoms will probably move.  The smaller the system, the
> larger
> > the effect will likely be.  Consider also what reference coordinates are
> > doing.  They define how strong the potential is (distance between current
> > coordinates and reference).  If you're scaling all atoms individually
> > according to the pressure coupling, the reference moves and therefore the
> > atoms can also move.  For larger systems like proteins,
> "refcoord_scaling =
> > com" is normal and stable, and "refcoord_scaling = all" is disfavored.
> >  Honestly, I don't know what to expect for a very small system like
> yours,
> > but it is likely to be affected to a greater extent.
> >
> > If the "all" option gives you a stable simulation that allow for proper
> > equilibration, then I doubt there is any real problem.
> >
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > 

Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Thanks, Mark. I actually ran the same system with "com" option for timestep
of 1 fs using latest gromacs version 4.6.5 (earlier version i used was
4.6.3) and interestingly, it's running fine, not at all blowing up.
Thanks
Chetan


On Tue, Apr 8, 2014 at 2:43 AM, Mark Abraham wrote:

> On Apr 8, 2014 12:14 AM, "Chetan Mahajan"  wrote:
> >
> > Hi,
> >
> > Thanks a lot. It is clearer, but I have questions, so this email:
> >
> > Why is option "none" not desirable, if we want to restrain positions of
> > atoms of crystal to specific points? Isn't the strain generated due to
> > atoms scaling but not reference coordinates helping?
>
> Only if the model can absorb that stress at the given time step, which
> might not be true with heavily coupled constraints.
>
> > Why is none option
> > better than "com"? Is the possible movement of crystal due to "com"
> option
> > desirable?
>
> I already offered a theory about com not working in your case.
>
> > If a particular option exists, then it does so for a particular purpose.
> In
> > which case, "none" or "all" be a valid option?
>
> These are all unphysical hacks, so "it was easy to implement and might be
> useful enough for something" is a valid purpose when building a general
> purpose tool. Probably protein use cases were considered, and not crystal
> structures. Do something that works and move on to real equilibration! :-)
>
> Mark
>
> > Thanks
> > Chetan
> >
> >
> > On Mon, Mar 24, 2014 at 10:40 PM, Christopher Neale <
> > chris.ne...@alum.utoronto.ca> wrote:
> >
> > > Say you have a box with an x-side length of 3 nm and two atoms with
> > > x-dimension position restraints to: (a) x=1 nm, and (b) x=2 nm
> > >
> > > Then let the box shrink to 99% of its previous size due to pressure
> > > coupling. The following is my understanding of  the locations to which
> the
> > > atoms will be restrained:
> > >
> > > refcoord_scaling =
> > >
> > > none:
> > > (a) x=1 nm, and (b) x=2 nm  -- note how the restraint positions are not
> > > scaled (even though the positions of the atoms are scaled due to
> pressure
> > > coupling)
> > >
> > > all:
> > > (a) x=0.99 nm, and (b) x=1.98 nm   -- note how the atoms are now
> > > restrained to be closer together
> > >
> > > com:
> > > (a) x=0.985 nm, and (b) x=1.985 nm  -- note how the distance between
> the
> > > atoms is maintained
> > >
> > >
> > > So you see how "none" leads to problems because the restraint reference
> > > positions are not scaled at all with the atomic positions and how "all"
> > > leads to problems because, if you restrained all Ca atoms, then you
> would
> > > get compression/expansion of the size of your protein as the system
> > > fluctuated in constant pressure simulations.
> > >
> > > Chris.
> > > 
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Chetan
> > > Mahajan 
> > > Sent: 24 March 2014 23:25
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] refcoord-scaling
> > >
> > > Thanks, Justin. I am trying to understand what is meant by 'com'
> option.
> > > Following two sentences in manual seem conflicting with each other:
> > >
> > > "*Scale* the center of mass of the reference coordinates with the
> scaling
> > > matrix of the pressure coupling. The *vectors of each reference
> > > coordinate*to the center of mass are *not
> > > scaled*."
> > >
> > > Doesn't scaling center of mass of reference coordinates change
> something
> > > else ? reference coordinates?
> > >
> > > Thanks
> > >
> > > Chetan
> > >
> > >
> > > On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul 
> wrote:
> > >
> > > >
> > > >
> > > > On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
> > > >
> > > >> Hi Justin,
> > > >>
> > > >> My system is TiO2 crystal (2160 atoms position restrained) solvated
> by
> > > >> 3656
> > > >> water molecules, 1 formate anion and 1 sodium ion.  Is it true that
> when
> > > >> 'all' option i

Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Hi Mark

We discussed this "refcoord scaling=com not working" quite a bit. With new
version of gromacs 4.6.5, it seemed that com option is working fine.
However, I later found out that it is only for equilibration run and system
does blow up (domain decomposition error) in production run. Again to
revise: I have a system consisting of 13133 atoms ( A TiO2 crystal ( 720
Ti) , 3656 water molecules, 1 formate ion, 1 sodium ion). Atoms in TiO2
crystal are held by position restraints.

In the following you had made a comment that multiple COM and PBC may not
be working well with each other. WHy did you think it's a case of
"multiple" com of TiO2?  I am asking this, since in my TiO2 crystal, we are
not defining any bonds between Ti and O, although we are defining entire
TiO2 crystal to be one molecule. So, we can think of only 1 com.

Thanks
Chetan



On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham wrote:

> On Mar 24, 2014 1:10 AM, "Chetan Mahajan"  wrote:
> >
> > Dear all:
> >
> > I am trying to get a simulation of water solvated titanium oxide running.
> > When 'all' option is used for refcoord-scaling, simulation runs ok.
> > However, when 'com' option is used for refcoord-scaling, simulation
> crashes
> > with any of the following errors. Could anyone explain to me why is this
> > happening
>
> See the description of com. You didn't tell us what you were restraining,
> so it's hard to help. But I can see multiple com of tio2 and PBC not
> working well together, particularly if you box size is far from best.
>
> > or when each of the options such as 'all', 'com' and 'no' is used?
>
> When you really care about your starting position and need to equilibrate
> in NPT.
>
> Mark
>
> > Thanks a lot!
> > regards
> > Chetan
> >
> >
> > Errors:
> >
> > X particles communicated to PME node Y are more than a cell length out of
> > the domain decomposition cell of their charge group
> >
> > This is another way that mdrun tells you your system is blowing
> > up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> > In GROMACS version 4.0, domain decomposition was introduced to divide the
> > system into regions containing nearby atoms (for more details, see the
> > manual <http://www.gromacs.org/Documentation/Manual> or the GROMACS 4
> > paper<http://dx.doi.org/10.1021/ct700301q>).
> > If you have particles that are flying across the system, you will get
> this
> > fatal error. The message indicates that some piece of your system is
> > tearing apart (hence out of the "cell of their charge group"). Refer
> > to the Blowing
> > Up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up> page
> for
> > advice on how to fix this issue.
> >
> >
> > A charge group moved too far between two domain decomposition steps.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] poor minimization?

[Chetan Mahajan]

Hi

I am simulating a system consisting of TiO2 crystal (2160 atoms position
restrained), 3656 water molecules, 1 formate and 1 sodium ion. All of my
energy minimizations (5000 steps or more) are getting over in few seconds
(both for steepest descent as well as conjugate gradient). Would you call
that a poor minimization with following data to add more information? If
yes, what could be done to improve it?

(Also note very high value of the maximum force in all trials)

Steepest Descents did not converge to Fmax < 10 in 5001 steps.
Potential Energy  = -1.8874660e+06
Maximum force =  9.7974286e+02 on atom 2161
Norm of force =  1.2869212e+01

Steepest Descents did not converge to Fmax < 10 in 5001 steps.
Potential Energy  = -1.8869792e+06
Maximum force =  2.2741604e+03 on atom 2161
Norm of force =  2.5534626e+01

Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
   F-max =  6.04871e+03 on atom 563
   F-Norm=  8.55788e+02

Thanks
Chetan
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[gmx-users] water stretched apart

[Chetan Mahajan]

Dear All,

I need help interpreting one image, that I am sharing via a link:

https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png

It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
molecules, totaling 13133 atoms overall. As you can see TiO2 slab is at the
center of the box. What I am concerned about is the few water molecules
stretched along a long distance (visible via lines) in the snapshot shared
above. Can anyone throw light on what does it mean or why it is happening?
Is it bad totally? Any solution, if it is totally bad?

I am using a timestep of 1 fs for entire simulation.

Thank you very much.

regards
Chetan
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Re: [gmx-users] water stretched apart

[Chetan Mahajan]

Thanks, Tsjerk. I tried it with following:

trjconv -pbc whole -f lnanop.xtc -s lnanop.tpr -o lnanoppbc.xtc

It gives the error : Cannot read from input

and

WARNING: If there are molecules in the input trajectory file
 that are broken across periodic boundaries, they
 cannot be made whole (or treated as whole) without
 you providing a run input file.

I read trjconv part of manual again and again, but can't figure out what's
going wrong. Could you help please?

Thanks
Chetan


On Sun, May 11, 2014 at 1:30 AM, Tsjerk Wassenaar  wrote:

> Hi Chetan,
>
> That's due to PBC. Use trjconv -pbc whole to fix it.
>
> Cheers,
>
> Tsjerk
> On May 11, 2014 8:12 AM, "Chetan Mahajan"  wrote:
>
> > Dear All,
> >
> > I need help interpreting one image, that I am sharing via a link:
> >
> >
> >
> https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png
> >
> > It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
> > refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
> > molecules, totaling 13133 atoms overall. As you can see TiO2 slab is at
> the
> > center of the box. What I am concerned about is the few water molecules
> > stretched along a long distance (visible via lines) in the snapshot
> shared
> > above. Can anyone throw light on what does it mean or why it is
> happening?
> > Is it bad totally? Any solution, if it is totally bad?
> >
> > I am using a timestep of 1 fs for entire simulation.
> >
> > Thank you very much.
> >
> > regards
> > Chetan
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] water stretched apart

[Chetan Mahajan]

Dear Chandan,

Yes, .tpr file is in the same folder. I am not sure what's happening.

Thanks
Chetan


On Sun, May 11, 2014 at 3:17 AM, Chandan Choudhury wrote:

> Dear Chetan,
> trjconv is finding difficult to find the trp file. Check that the tpr
> yourare providing is in the right place.
>
> Chandan
> On Sun, May 11, 2014 at 1:33 PM, Chetan Mahajan  >wrote:
>
> > Thanks, Tsjerk. I tried it with following:
> >
> > trjconv -pbc whole -f lnanop.xtc -s lnanop.tpr -o lnanoppbc.xtc
> >
> > It gives the error : Cannot read from input
> >
> > and
> >
> > WARNING: If there are molecules in the input trajectory file
> >  that are broken across periodic boundaries, they
> >  cannot be made whole (or treated as whole) without
> >  you providing a run input file.
> >
> > I read trjconv part of manual again and again, but can't figure out
> what's
> > going wrong. Could you help please?
> >
> > Thanks
> > Chetan
> >
> >
> > On Sun, May 11, 2014 at 1:30 AM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi Chetan,
> > >
> > > That's due to PBC. Use trjconv -pbc whole to fix it.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > > On May 11, 2014 8:12 AM, "Chetan Mahajan" 
> wrote:
> > >
> > > > Dear All,
> > > >
> > > > I need help interpreting one image, that I am sharing via a link:
> > > >
> > > >
> > > >
> > >
> >
> https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png
> > > >
> > > > It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
> > > > refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
> > > > molecules, totaling 13133 atoms overall. As you can see TiO2 slab is
> > at
> > > the
> > > > center of the box. What I am concerned about is the few water
> > molecules
> > > > stretched along a long distance (visible via lines) in the snapshot
> > > shared
> > > > above. Can anyone throw light on what does it mean or why it is
> > > happening?
> > > > Is it bad totally? Any solution, if it is totally bad?
> > > >
> > > > I am using a timestep of 1 fs for entire simulation.
> > > >
> > > > Thank you very much.
> > > >
> > > > regards
> > > > Chetan
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> > > >
> > > --
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> > >
> > --
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>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
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[gmx-users] crystal slab and position restraints: com option

[Chetan Mahajan]

Dear All,

I am new to GROMACS. I am simulating TiO2 crystal slab (2160 atoms, slab
dimensions:  30.63 A0 x 37.76 A0 x 21.05 A0) solvated by 3656 water
molecules, 1 sodium ion and 1 formate ion. I am applying position
restraints to each Ti and O with refcoord-scaling: com. With com option, we
expect crystal to not change in dimensions, but my crystal slab dimensions
after equilibrium and production runs are 29.82 A0 x 35.91 A0 x 19.52 A0.
So we see that slab has shrinked. Is this okay?

Thank you very much.

regards
Chetan
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Re: [gmx-users] crystal slab and position restraints: com option

[Chetan Mahajan]

Thanks, Justin. I was also under impression that with "com" option,
distance between slab atoms (which are position restrained) remains same,
even though coordinates change. So doesn't it mean that TiO2 slab
dimensions should remain same?

Thanks a lot
regards
Chetan


On Sun, May 11, 2014 at 12:55 PM, Justin Lemkul  wrote:

>
>
> On 5/11/14, 1:51 PM, Chetan Mahajan wrote:
>
>> Dear All,
>>
>> I am new to GROMACS. I am simulating TiO2 crystal slab (2160 atoms, slab
>> dimensions:  30.63 A0 x 37.76 A0 x 21.05 A0) solvated by 3656 water
>> molecules, 1 sodium ion and 1 formate ion. I am applying position
>> restraints to each Ti and O with refcoord-scaling: com. With com option,
>> we
>> expect crystal to not change in dimensions, but my crystal slab dimensions
>> after equilibrium and production runs are 29.82 A0 x 35.91 A0 x 19.52 A0.
>> So we see that slab has shrinked. Is this okay?
>>
>>
> Using NPT, the box dimensions will change.  The "refcoord-scaling = com"
> option means the resulting positions are scaled based on the COM of their
> reference positions.  None of those conditions would suggest the box or
> coordinates won't change.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] multiple molecules of same type and .top file

[Chetan Mahajan]

Dear All,

I am trying to generate .top file for my system. I would be obliged if you
could explain following topology file question to me, since it is not very
clearly mentioned anywhere:

In LAMMPS software that I am used to, user is required to enter details of
topology for all the molecules of same type e.g. if there are 1000 formate
ions, one needs to enter atoms, bonds, angles, dihedrals for all 1000
formate ions. Is this the case for GROMACS or only one representational
topology for 1 molecule of that type is sufficient? Atoms section in .top
file in gromacs does contain column for residue number (resi or resnr) in a
given [moleculetype], so I would guess probably I need to enter all the
molecules of a given type, although it is not the case for water?

Thanks a lot!

regards
Chetan
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[gmx-users] confirm please

[Chetan Mahajan]

Dear All,

I am using amber2gromacs tool acpype for converting input files for AMBER
into those for GROMACS. There are some differences in these files (.gro and
.top) compared to the information given in gromacs manual 4.6.5 abotu these
kind of files.

First, while listing charges and vander waals parameters for all the atom
types in [atomtypes] directive, there is no second column titled as
"at.num" in the manual. Is that okay? What does that column mean anyways
(number of atoms of that type?)?

Second, where there is atom name and number to be mentioned for each atom
in a given molecule in .gro file,
numbering is not consecutively for all atoms as mentioned in the manual.
E.g. instead of OW1, HW1 and HW2 for water, it is just O, H1 and H2.
Instead of O1, O2 in formate, it's just O, O1.

>From my understanding, it seems okay, as long as atom name and number
(identity of that atom) is same in .gro as well as .top. However, I just
wanted to confirm it.

Thanks in advance!

regards
Chetan
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Re: [gmx-users] confirm please

[Chetan Mahajan]

gromacs is not giving error, but just wanted to confirm, especially the
first question. In absence of column for at.num, how would gromacs reading
my file know that second column is for mass? It's ofcourse commented as to
mass, but comments are not read anyways.

Thanks
Chetan


On Mon, May 12, 2014 at 6:32 PM, Chetan Mahajan wrote:

> Dear All,
>
> I am using amber2gromacs tool acpype for converting input files for AMBER
> into those for GROMACS. There are some differences in these files (.gro and
> .top) compared to the information given in gromacs manual 4.6.5 abotu these
> kind of files.
>
> First, while listing charges and vander waals parameters for all the atom
> types in [atomtypes] directive, there is no second column titled as
> "at.num" in the manual. Is that okay? What does that column mean anyways
> (number of atoms of that type?)?
>
> Second, where there is atom name and number to be mentioned for each atom
> in a given molecule in .gro file,
> numbering is not consecutively for all atoms as mentioned in the manual.
> E.g. instead of OW1, HW1 and HW2 for water, it is just O, H1 and H2.
> Instead of O1, O2 in formate, it's just O, O1.
>
> From my understanding, it seems okay, as long as atom name and number
> (identity of that atom) is same in .gro as well as .top. However, I just
> wanted to confirm it.
>
> Thanks in advance!
>
> regards
> Chetan
>
>
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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Thanks, Mark. With timestep to be 1 fs (instead of 2 fs) in production run,
job is running fine without blowing up. (equilibration run also contains
timestep to be 1 fs and refcoord-scaling option is set to "com"). However,
time step to 1 fs in production run does not affect water and its
relaxation, since water is kept rigid.

Now I have a question: Having to make nstlist option as "1" or reducing
timestep to "1 fs" to make the job run without blowing up, does this mean
everything scientifically is okay? In other words, do these changes
suppress any other serious error, with respect to forcefield choice eg.?

Thanks
Chetan


On Mon, May 12, 2014 at 11:53 PM, Mark Abraham wrote:

>
> On May 10, 2014 10:00 PM, "Chetan Mahajan"  wrote:
> >
> > Hi Mark
> >
> > We discussed this "refcoord scaling=com not working" quite a bit. With
> new version of gromacs 4.6.5, it seemed that com option is working fine.
> However, I later found out that it is only for equilibration run and system
> does blow up (domain decomposition error) in production run. Again to
> revise: I have a system consisting of 13133 atoms ( A TiO2 crystal ( 720
> Ti) , 3656 water molecules, 1 formate ion, 1 sodium ion). Atoms in TiO2
> crystal are held by position restraints.
>
> Doing something artificial during equilibration and then turning it off
> can lead to abrupt changes of behavior because you were not equilibrated at
> the new regime. If you have a valid model for the crystal, you should be
> able to equilibrate without needing to use artificial restraints that were
> never designed for your use case. That might mean tiny time steps to relax
> water molecules, or gradual heating stages, or taking care to choose a
> valid volume in the first place.
>
> > In the following you had made a comment that multiple COM and PBC may
> not be working well with each other. WHy did you think it's a case of
> "multiple" com of TiO2?  I am asking this, since in my TiO2 crystal, we are
> not defining any bonds between Ti and O, although we are defining entire
> TiO2 crystal to be one molecule. So, we can think of only 1 com.
>
> Depends how you implemented the crystal. If there's lots of repeated TiO2
> moleculetypes, or such, then there are multiple com because grompp doesn't
> get told about the higher-order picture.
>
> Even if you have a single molecule for the whole crystal, I would not bet
> that the implementation of position restraints in NPT is well tested in the
> case of a restrained atom crossing a periodic boundary. Probably only
> compact protein solutes far from boundaries were tested. That might not be
> relevant in your case, and it might be implemented "right" after all, but
> you are warned that you should not blindly expect too much, here.
>
> Mark
>
> > Thanks
> > Chetan
> >
> >
> >
> > On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham 
> wrote:
> >>
> >> On Mar 24, 2014 1:10 AM, "Chetan Mahajan"  wrote:
> >> >
> >> > Dear all:
> >> >
> >> > I am trying to get a simulation of water solvated titanium oxide
> running.
> >> > When 'all' option is used for refcoord-scaling, simulation runs ok.
> >> > However, when 'com' option is used for refcoord-scaling, simulation
> >> crashes
> >> > with any of the following errors. Could anyone explain to me why is
> this
> >> > happening
> >>
> >> See the description of com. You didn't tell us what you were
> restraining,
> >> so it's hard to help. But I can see multiple com of tio2 and PBC not
> >> working well together, particularly if you box size is far from best.
> >>
> >> > or when each of the options such as 'all', 'com' and 'no' is used?
> >>
> >> When you really care about your starting position and need to
> equilibrate
> >> in NPT.
> >>
> >> Mark
> >>
> >> > Thanks a lot!
> >> > regards
> >> > Chetan
> >> >
> >> >
> >> > Errors:
> >> >
> >> > X particles communicated to PME node Y are more than a cell length
> out of
> >> > the domain decomposition cell of their charge group
> >> >
> >> > This is another way that mdrun tells you your system is blowing
> >> > up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
> >> > In GROMACS version 4.0, domain decomposition was introduced to divide
> the
> >> > system into regions containing n

Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Thanks, Mark. What do you mean by buffer in your last sentence?


On Tue, May 13, 2014 at 1:00 AM, Mark Abraham wrote:

>
> On May 13, 2014 7:34 AM, "Chetan Mahajan"  wrote:
> >
> > Thanks, Mark. With timestep to be 1 fs (instead of 2 fs) in production
> run, job is running fine without blowing up. (equilibration run also
> contains timestep to be 1 fs and refcoord-scaling option is set to "com").
> However, time step to 1 fs in production run does not affect water and its
> relaxation, since water is kept rigid.
>
> Sounds like maybe the TiO2 model is not stable.
>
> > Now I have a question: Having to make nstlist option as "1" or reducing
> timestep to "1 fs" to make the job run without blowing up, does this mean
> everything scientifically is okay? In other words, do these changes
> suppress any other serious error, with respect to forcefield choice eg.?
>
> Validating a model can only be done a posteriori, by observing whether it
> reproduces the right ensemble. Reducing the time step generally improves
> the quality with which the integrator produces the (shadow) ensemble (but
> there are lots of subtle effects) - it says nothing about the quality of
> the ensemble, though.
>
> Nstlist should never need to be 1 if you are using a buffer in that list;
> doing so will generally improve performance. Details vary with your
> nonbonded setup.
>
> Mark
>
> > Thanks
> > Chetan
> >
> >
> > On Mon, May 12, 2014 at 11:53 PM, Mark Abraham 
> wrote:
> >>
> >>
> >> On May 10, 2014 10:00 PM, "Chetan Mahajan" 
> wrote:
> >> >
> >> > Hi Mark
> >> >
> >> > We discussed this "refcoord scaling=com not working" quite a bit.
> With new version of gromacs 4.6.5, it seemed that com option is working
> fine. However, I later found out that it is only for equilibration run and
> system does blow up (domain decomposition error) in production run. Again
> to revise: I have a system consisting of 13133 atoms ( A TiO2 crystal ( 720
> Ti) , 3656 water molecules, 1 formate ion, 1 sodium ion). Atoms in TiO2
> crystal are held by position restraints.
> >>
> >> Doing something artificial during equilibration and then turning it off
> can lead to abrupt changes of behavior because you were not equilibrated at
> the new regime. If you have a valid model for the crystal, you should be
> able to equilibrate without needing to use artificial restraints that were
> never designed for your use case. That might mean tiny time steps to relax
> water molecules, or gradual heating stages, or taking care to choose a
> valid volume in the first place.
> >>
> >> > In the following you had made a comment that multiple COM and PBC may
> not be working well with each other. WHy did you think it's a case of
> "multiple" com of TiO2?  I am asking this, since in my TiO2 crystal, we are
> not defining any bonds between Ti and O, although we are defining entire
> TiO2 crystal to be one molecule. So, we can think of only 1 com.
> >>
> >> Depends how you implemented the crystal. If there's lots of repeated
> TiO2 moleculetypes, or such, then there are multiple com because grompp
> doesn't get told about the higher-order picture.
> >>
> >> Even if you have a single molecule for the whole crystal, I would not
> bet that the implementation of position restraints in NPT is well tested in
> the case of a restrained atom crossing a periodic boundary. Probably only
> compact protein solutes far from boundaries were tested. That might not be
> relevant in your case, and it might be implemented "right" after all, but
> you are warned that you should not blindly expect too much, here.
> >>
> >> Mark
> >>
> >> > Thanks
> >> > Chetan
> >> >
> >> >
> >> >
> >> > On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham <
> mark.j.abra...@gmail.com> wrote:
> >> >>
> >> >> On Mar 24, 2014 1:10 AM, "Chetan Mahajan" 
> wrote:
> >> >> >
> >> >> > Dear all:
> >> >> >
> >> >> > I am trying to get a simulation of water solvated titanium oxide
> running.
> >> >> > When 'all' option is used for refcoord-scaling, simulation runs ok.
> >> >> > However, when 'com' option is used for refcoord-scaling, simulation
> >> >> crashes
> >> >> > with any of the following errors. Could anyone explain to me why
> is this
> >> >> > happe

[gmx-users] amber to gromacs conversion

[Chetan Mahajan]

Dear All,

While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:

sigma = 2 * r * 2^(-1/6)

I understand the factor 2^(-1/6), but there is another "2" that appears in
the beginning. Where is that factor coming from? That factor does not arise
when we choose following forms for LJ potential functions in Amber as well
as Gromacs.

Amber:

[image: Inline image 1]

Gromacs:

[image: Inline image 2]

Thanks in advance!

regards
Chetan
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[gmx-users] amber to gromacs conversion of LJ potential

[Chetan Mahajan]

Dear All,

While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:

sigma = 2 * r * 2^(-1/6)

I understand the factor 2^(-1/6), but there is another "2" that appears in
the beginning. Where is that factor coming from? That factor does not arise
when we choose following forms for LJ potential functions in Amber as well
as Gromacs.

Amber:

[image: Inline image 1]

Gromacs:

[image: Inline image 2]

Thanks in advance!

regards
Chetan
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[gmx-users] small questions on tabulated functions

[Chetan Mahajan]

Dear All,

I just came across this fantastic capability of Gromacs, Tabulated
functions, which can let me use LJ potential for some atom pairs whereas
Buckingham for some others. However, I have a doubt about topology file
construction, even after reading a document by Gareth and going through
earlier posts on this mail-list. I would be highly obliged if anyone can
help:

1) Specifically, since I have LJ and buckingham both, do need to repeat
nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1 followed by LJ
parameters  C and A for the concerned pairs and then nbfunc=2 , followed by
buckingham parameters C, A , B for concerned pairs in the .top file?

Besides,

2) I guess the order of parameters for Buckingham potential in .top file
would be C, A and B (for the expression in section 4.1.2 and page 69 of the
manual-4.6.5).  Please comment if not so.

3) Is there a way to turn off selection of combination rule totally? This
is since I have all the cross terms for LJ as well as buckingham pairs
myself (it's not advisable to allow direct combination rule, since e.g.
atom X interacts with Y using buckingham, while same atom X interacts with
Z using LJ). I hope there cross terms overwrite comb-rule selection, in
which case, comb-rule specification does not matter.

Thanks in advance!

regards
Chetan
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Re: [gmx-users] small questions on tabulated functions

[Chetan Mahajan]

Dear All,

Now I do understand the answer to Q 3 in the earlier email that explicit
cross terms will overwrite mixing rule , after reading through the part of
document, missed earlier. Please advise on Q 1 and 2 in the
earlier/following email.

Thank you very much.

regards
Chetan


On Tue, May 27, 2014 at 3:58 AM, Chetan Mahajan wrote:

> Dear All,
>
> I just came across this fantastic capability of Gromacs, Tabulated
> functions, which can let me use LJ potential for some atom pairs whereas
> Buckingham for some others. However, I have a doubt about topology file
> construction, even after reading a document by Gareth and going through
> earlier posts on this mail-list. I would be highly obliged if anyone can
> help:
>
> 1) Specifically, since I have LJ and buckingham both, do need to repeat
> nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1 followed by LJ
> parameters  C and A for the concerned pairs and then nbfunc=2 , followed by
> buckingham parameters C, A , B for concerned pairs in the .top file?
>
> Besides,
>
> 2) I guess the order of parameters for Buckingham potential in .top file
> would be C, A and B (for the expression in section 4.1.2 and page 69 of the
> manual-4.6.5).  Please comment if not so.
>
> 3) Is there a way to turn off selection of combination rule totally? This
> is since I have all the cross terms for LJ as well as buckingham pairs
> myself (it's not advisable to allow direct combination rule, since e.g.
> atom X interacts with Y using buckingham, while same atom X interacts with
> Z using LJ). I hope there cross terms overwrite comb-rule selection, in
> which case, comb-rule specification does not matter.
>
> Thanks in advance!
>
> regards
> Chetan
>
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[gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

Dear All,

I just came across this fantastic capability of Gromacs, user-specified
potential functions, which can let me use LJ potential for some atom pairs
whereas Buckingham for some others. However, I have a doubt about topology
file construction, even after reading a document by Gareth and going
through earlier posts on this mail-list. I would be highly obliged if
anyone can help:

Specifically, since I have LJ and buckingham both, do need to repeat
statement mentioning nbfunc ( and combination-rule) in .top file? e.g.
nbfunc=1 followed by LJ parameters  C and A for the concerned pairs and
then nbfunc=2 (and whatever combination rule) , followed by buckingham
parameters C, A , B for concerned pairs in the .top file?

Thanks a lot!

regards
Chetan
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Re: [gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

Hi Mark and Justin,

File written by Gareth Tribello and attached to the end of following page
on GROMACS site discusses how one can specify buckingham interaction for Na
Na and Cl Cl while still specifying Lennard-Jone interaction between Na and
Cl. (page last modified on 9th Feb 2014 by Justin.)

http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s


File by Gareth Tribello mentions example of NaCl, where interaction Na Na
and Cl Cl is buckingham, whereas interaction Na Cl is LJ. But it's not
clear what should one specify nbfunc and comb-rule as, in a .top file.

Also, let me share in the following, paragraph from section 6.9.2 of
Gromacs manual 4.6.5:

"If you want to have different functional forms between different groups of
atoms, this can be set through energy groups. Different tables can be used
for non-bonded interactions between different energy groups pairs through
the .mdp option energygrp-table (see sec. 7.3). Atoms that should interact
with a different potential should be put into different energy groups.
Between group pairs which are not listed in energygrp-table, the normal
user tables will be used. This makes it easy to use a different functional
form between a few types of atoms."

All of this does point out that one can mix LJ and buckingham amongst
different pairs of atoms. e.g. A and B could interact via LJ potential,
whereas A and C (say C is bonded to B) interact via buckingham potential.

Thanks
Chetan


On Thu, May 29, 2014 at 12:51 AM, Mark Abraham 
wrote:

> Hi,
>
> I do not think there is any ability in GROMACS to mix LJ and Buckingham.
> Each particle can have only one set of non-bonded parameters, so there is
> no sensible way to express the interaction between the sets of atoms
> natively using each type of interaction.
>
> Mark
> On May 29, 2014 2:28 AM, "Chetan Mahajan"  wrote:
>
> > Dear All,
> >
> > I just came across this fantastic capability of Gromacs, user-specified
> > potential functions, which can let me use LJ potential for some atom
> pairs
> > whereas Buckingham for some others. However, I have a doubt about
> topology
> > file construction, even after reading a document by Gareth and going
> > through earlier posts on this mail-list. I would be highly obliged if
> > anyone can help:
> >
> > Specifically, since I have LJ and buckingham both, do need to repeat
> > statement mentioning nbfunc ( and combination-rule) in .top file? e.g.
> > nbfunc=1 followed by LJ parameters  C and A for the concerned pairs and
> > then nbfunc=2 (and whatever combination rule) , followed by buckingham
> > parameters C, A , B for concerned pairs in the .top file?
> >
> > Thanks a lot!
> >
> > regards
> > Chetan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

I forgot to say, but I look forward to hearing from both of you, with any
comments on my understanding.

Thanks
Chetan


On Thu, May 29, 2014 at 12:51 PM, Chetan Mahajan 
wrote:

> Hi Mark and Justin,
>
> File written by Gareth Tribello and attached to the end of following page
> on GROMACS site discusses how one can specify buckingham interaction for Na
> Na and Cl Cl while still specifying Lennard-Jone interaction between Na and
> Cl. (page last modified on 9th Feb 2014 by Justin.)
>
>
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s
>
>
> File by Gareth Tribello mentions example of NaCl, where interaction Na Na
> and Cl Cl is buckingham, whereas interaction Na Cl is LJ. But it's not
> clear what should one specify nbfunc and comb-rule as, in a .top file.
>
> Also, let me share in the following, paragraph from section 6.9.2 of
> Gromacs manual 4.6.5:
>
> "If you want to have different functional forms between different groups
> of atoms, this can be set through energy groups. Different tables can be
> used for non-bonded interactions between different energy groups pairs
> through the .mdp option energygrp-table (see sec. 7.3). Atoms that should
> interact with a different potential should be put into different energy
> groups. Between group pairs which are not listed in energygrp-table, the
> normal user tables will be used. This makes it easy to use a different
> functional form between a few types of atoms."
>
> All of this does point out that one can mix LJ and buckingham amongst
> different pairs of atoms. e.g. A and B could interact via LJ potential,
> whereas A and C (say C is bonded to B) interact via buckingham potential.
>
> Thanks
> Chetan
>
>
> On Thu, May 29, 2014 at 12:51 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> I do not think there is any ability in GROMACS to mix LJ and Buckingham.
>> Each particle can have only one set of non-bonded parameters, so there is
>> no sensible way to express the interaction between the sets of atoms
>> natively using each type of interaction.
>>
>> Mark
>> On May 29, 2014 2:28 AM, "Chetan Mahajan"  wrote:
>>
>> > Dear All,
>> >
>> > I just came across this fantastic capability of Gromacs, user-specified
>> > potential functions, which can let me use LJ potential for some atom
>> pairs
>> > whereas Buckingham for some others. However, I have a doubt about
>> topology
>> > file construction, even after reading a document by Gareth and going
>> > through earlier posts on this mail-list. I would be highly obliged if
>> > anyone can help:
>> >
>> > Specifically, since I have LJ and buckingham both, do need to repeat
>> > statement mentioning nbfunc ( and combination-rule) in .top file? e.g.
>> > nbfunc=1 followed by LJ parameters  C and A for the concerned pairs and
>> > then nbfunc=2 (and whatever combination rule) , followed by buckingham
>> > parameters C, A , B for concerned pairs in the .top file?
>> >
>> > Thanks a lot!
>> >
>> > regards
>> > Chetan
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>>
>
>
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Re: [gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

Thanks. So let me rephrase so that I get your point:

I reread the document by Gareth. As described in section 2 (changing the
form of global interaction), nbfunc is set to 1, even if potential is of
6-9 form instead of 6-12 form of Lennard Jones. Now, even for buckingham,
only C and A need to be provided, since B can be clubbed with function of r
i.e. exp(-B*r), as you mentioned in the beginning of last email of yours
(although the *source of the confusion was the note 1 on the bottom of page
2 of this document*, which says 3 parameters A, B and C need to be provided
for buckingham). Thus, nbfunc=1 should work even if some pairs interact via
buckingham while others by LJ.

Please comment.

Thanks
Chetan


On Fri, May 30, 2014 at 12:02 AM, Mark Abraham 
wrote:

> On May 29, 2014 2:28 AM, "Chetan Mahajan"  wrote:
> >
> > Dear All,
> >
> > I just came across this fantastic capability of Gromacs, user-specified
> > potential functions, which can let me use LJ potential for some atom
> pairs
> > whereas Buckingham for some others. However, I have a doubt about
> topology
> > file construction, even after reading a document by Gareth and going
> > through earlier posts on this mail-list. I would be highly obliged if
> > anyone can help:
> >
> > Specifically, since I have LJ and buckingham both, do need to repeat
> > statement mentioning nbfunc ( and combination-rule) in .top file? e.g.
> > nbfunc=1 followed by LJ parameters  C and A for the concerned pairs and
> > then nbfunc=2 (and whatever combination rule) , followed by buckingham
> > parameters C, A , B for concerned pairs in the .top file?
>
> Gareth's approach relies on absorbing the extra parameter for Buckingham
> into h(r) of the table and specifying which tables are used by which pairs
> of atom types. That should work, but IIRC is capped by the allowed number
> of energy groups, probably 64. My earlier point was that GROMACS can only
> do the same thing with the parameters for the two interaction types right
> up to the point the table is used, so you must express in the topology the
> right values for whichever nbfunc value you choose as convenient. You can't
> choose a second value for nbfunc anywhere. Depending on your values and
> combination rule, you might need to absorb a scaling factor into g(r) or
> h(r), too!
>
> Mark
>
> > Thanks a lot!
> >
> > regards
> > Chetan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

Here is one more thing (hopefully last!):   If you have 8 energy groups,
there are lot of cross terms as you see. Some of these cross terms have to
be described by specific tables for each of those pairs. However, many
other pairs do not need specific tables, so a general table.xvg (not
specified by energygrp-table option), which is for pure LJ interaction in
my simulations, would suffice. Now, is it mandatory that I need to
explicitly provide LJ parameters for all of these remaining pairs (too many
!) or Gromacs will calculate those using combination rule and then apply
table.xvg, as it is intended to apply to a non-specific pair? I feel
Gromacs should be able to calculate cross term and apply table.xvg, without
the need to enter C an A for that pair explicitly as an additional term in
topology file. I need to confirm.

Thanks
Chetan


On Fri, May 30, 2014 at 2:38 AM, Mark Abraham 
wrote:

> Yes. Three parameters are needed for nbfunc 2 in order to use the few
> kernels that implement Buckingham; using a Buckingham-shaped table with
> nbfunc 1 is not "using Buckingham" from the point of view of how many
> parameters grompp will expect.
>
> Mark
> On May 30, 2014 8:19 AM, "Chetan Mahajan"  wrote:
>
> > Thanks. So let me rephrase so that I get your point:
> >
> > I reread the document by Gareth. As described in section 2 (changing the
> > form of global interaction), nbfunc is set to 1, even if potential is of
> > 6-9 form instead of 6-12 form of Lennard Jones. Now, even for buckingham,
> > only C and A need to be provided, since B can be clubbed with function
> of r
> > i.e. exp(-B*r), as you mentioned in the beginning of last email of yours
> > (although the *source of the confusion was the note 1 on the bottom of
> page
> > 2 of this document*, which says 3 parameters A, B and C need to be
> provided
> > for buckingham). Thus, nbfunc=1 should work even if some pairs interact
> via
> > buckingham while others by LJ.
> >
> > Please comment.
> >
> > Thanks
> > Chetan
> >
> >
> > On Fri, May 30, 2014 at 12:02 AM, Mark Abraham  >
> > wrote:
> >
> > > On May 29, 2014 2:28 AM, "Chetan Mahajan" 
> wrote:
> > > >
> > > > Dear All,
> > > >
> > > > I just came across this fantastic capability of Gromacs,
> user-specified
> > > > potential functions, which can let me use LJ potential for some atom
> > > pairs
> > > > whereas Buckingham for some others. However, I have a doubt about
> > > topology
> > > > file construction, even after reading a document by Gareth and going
> > > > through earlier posts on this mail-list. I would be highly obliged if
> > > > anyone can help:
> > > >
> > > > Specifically, since I have LJ and buckingham both, do need to repeat
> > > > statement mentioning nbfunc ( and combination-rule) in .top file?
> e.g.
> > > > nbfunc=1 followed by LJ parameters  C and A for the concerned pairs
> and
> > > > then nbfunc=2 (and whatever combination rule) , followed by
> buckingham
> > > > parameters C, A , B for concerned pairs in the .top file?
> > >
> > > Gareth's approach relies on absorbing the extra parameter for
> Buckingham
> > > into h(r) of the table and specifying which tables are used by which
> > pairs
> > > of atom types. That should work, but IIRC is capped by the allowed
> number
> > > of energy groups, probably 64. My earlier point was that GROMACS can
> only
> > > do the same thing with the parameters for the two interaction types
> right
> > > up to the point the table is used, so you must express in the topology
> > the
> > > right values for whichever nbfunc value you choose as convenient. You
> > can't
> > > choose a second value for nbfunc anywhere. Depending on your values and
> > > combination rule, you might need to absorb a scaling factor into g(r)
> or
> > > h(r), too!
> > >
> > > Mark
> > >
> > > > Thanks a lot!
> > > >
> > > > regards
> > > > Chetan
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_g

Re: [gmx-users] help please @User-specified potential functions

[Chetan Mahajan]

Hmm. Gareth Tribello does say on the page 5 of that document:

 As for the cross terms, unless you have specific reason to believe that
gromacs will mix the terms correctly using mixing rule 1, you must provide
these explicitly in the [ nonbond params ] section immediately after the [
atomtypes ] section as follows:

I do not know why he thinks gromacs may not mix the terms correctly.
Thanks
Chetan

On Sat, May 31, 2014 at 8:43 AM, Mark Abraham 
wrote:

> I don't know. Confirmation is best done by testing it. Use mdrun -rerun and
> vary parameters and tables until you are satisfied you understand how it
> works.
>
> Mark
> On May 31, 2014 1:44 AM, "Chetan Mahajan"  wrote:
>
> > Here is one more thing (hopefully last!):   If you have 8 energy groups,
> > there are lot of cross terms as you see. Some of these cross terms have
> to
> > be described by specific tables for each of those pairs. However, many
> > other pairs do not need specific tables, so a general table.xvg (not
> > specified by energygrp-table option), which is for pure LJ interaction in
> > my simulations, would suffice. Now, is it mandatory that I need to
> > explicitly provide LJ parameters for all of these remaining pairs (too
> many
> > !) or Gromacs will calculate those using combination rule and then apply
> > table.xvg, as it is intended to apply to a non-specific pair? I feel
> > Gromacs should be able to calculate cross term and apply table.xvg,
> without
> > the need to enter C an A for that pair explicitly as an additional term
> in
> > topology file. I need to confirm.
> >
> > Thanks
> > Chetan
> >
> >
> > On Fri, May 30, 2014 at 2:38 AM, Mark Abraham 
> > wrote:
> >
> > > Yes. Three parameters are needed for nbfunc 2 in order to use the few
> > > kernels that implement Buckingham; using a Buckingham-shaped table with
> > > nbfunc 1 is not "using Buckingham" from the point of view of how many
> > > parameters grompp will expect.
> > >
> > > Mark
> > > On May 30, 2014 8:19 AM, "Chetan Mahajan" 
> wrote:
> > >
> > > > Thanks. So let me rephrase so that I get your point:
> > > >
> > > > I reread the document by Gareth. As described in section 2 (changing
> > the
> > > > form of global interaction), nbfunc is set to 1, even if potential is
> > of
> > > > 6-9 form instead of 6-12 form of Lennard Jones. Now, even for
> > buckingham,
> > > > only C and A need to be provided, since B can be clubbed with
> function
> > > of r
> > > > i.e. exp(-B*r), as you mentioned in the beginning of last email of
> > yours
> > > > (although the *source of the confusion was the note 1 on the bottom
> of
> > > page
> > > > 2 of this document*, which says 3 parameters A, B and C need to be
> > > provided
> > > > for buckingham). Thus, nbfunc=1 should work even if some pairs
> interact
> > > via
> > > > buckingham while others by LJ.
> > > >
> > > > Please comment.
> > > >
> > > > Thanks
> > > > Chetan
> > > >
> > > >
> > > > On Fri, May 30, 2014 at 12:02 AM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > > >
> > > > wrote:
> > > >
> > > > > On May 29, 2014 2:28 AM, "Chetan Mahajan" 
> > > wrote:
> > > > > >
> > > > > > Dear All,
> > > > > >
> > > > > > I just came across this fantastic capability of Gromacs,
> > > user-specified
> > > > > > potential functions, which can let me use LJ potential for some
> > atom
> > > > > pairs
> > > > > > whereas Buckingham for some others. However, I have a doubt about
> > > > > topology
> > > > > > file construction, even after reading a document by Gareth and
> > going
> > > > > > through earlier posts on this mail-list. I would be highly
> obliged
> > if
> > > > > > anyone can help:
> > > > > >
> > > > > > Specifically, since I have LJ and buckingham both, do need to
> > repeat
> > > > > > statement mentioning nbfunc ( and combination-rule) in .top file?
> > > e.g.
> > > > > > nbfunc=1 followed by LJ parameters  C and A for the concerned
> pairs
> > > and
> > > > > > then nbfunc=2 (and whatever combination rule) , followed by
> > > buckingham

[gmx-users] crystal, nrexcl

[Chetan Mahajan]

Dear All,

I have TiO2 crystal, in which bonds are not defined. Thus, I think "nrexcl"
term in the [moleculetype] section of topology file would be rendered not
meaningful at all. Any value there for nrexcl (I currently have it as 3)
would not really matter. Could you confirm this please? I ideally I would
not want any nonbonded interactions (even if between neighboring atoms)
excluded at all, since I do not have any bonds.

Thanks
Chetan
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[gmx-users] help needed

[Chetan Mahajan]

Dear All,

I am testing my gromacs code using user-specified potential functions (LJ
as well as Buckingham as non-bonded potentials). *Minimization run with
these potentials runs fine*. However, equilibration run gives following
error at which I am clueless. Could anyone help? Is it because total charge
is -0.018 and not zero?

...

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
starting mdrun 'tio2_formate'
100 steps,   1000.0 ps.
[c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught
error: Segmentation fault (signal 11)
[c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected
End-Of-File on file descriptor 7. MPI process died?
[c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error
while reading PMI socket. MPI process died?
[c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process
(rank: 5, pid: 122921) terminated with signal 11 -> abort job
[c418-701.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection]
mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4)
[c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while
reading PMI socket. MPI process died?
[c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
End-Of-File on file descriptor 21. MPI process died?
[c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while
reading PMI socket. MPI process died?
TACC: MPI job exited with code: 1

TACC: Shutdown complete. Exiting.


NOTE 1 [file lnanopf3.top, line 4422]:
  System has non-zero total charge: -0.018000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.




---
Program grompp, VERSION 4.6.5
Source code file:
/work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line:
593

File input/output error:
/work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro

...

Thanks a lot!

regards
Chetan
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Re: [gmx-users] help needed

[Chetan Mahajan]

More information:

As the log file shows, coulomb interaction energy is shooting to nan during
equilibration where error occurs. Coulomb interaction energy during
minimization is finite.

Thanks
Chetan


On Sun, Jun 1, 2014 at 4:44 PM, Chetan Mahajan  wrote:

> Dear All,
>
> I am testing my gromacs code using user-specified potential functions (LJ
> as well as Buckingham as non-bonded potentials). *Minimization run with
> these potentials runs fine*. However, equilibration run gives following
> error at which I am clueless. Could anyone help? Is it because total charge
> is -0.018 and not zero?
>
> ...
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
> starting mdrun 'tio2_formate'
> 100 steps,   1000.0 ps.
> [c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught
> error: Segmentation fault (signal 11)
> [c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected
> End-Of-File on file descriptor 7. MPI process died?
> [c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error
> while reading PMI socket. MPI process died?
> [c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process
> (rank: 5, pid: 122921) terminated with signal 11 -> abort job
> [c418-701.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection]
> mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4)
> [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
> End-Of-File on file descriptor 21. MPI process died?
> [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
> End-Of-File on file descriptor 21. MPI process died?
> [c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error
> while reading PMI socket. MPI process died?
> [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
> End-Of-File on file descriptor 21. MPI process died?
> [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
> End-Of-File on file descriptor 21. MPI process died?
> [c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error
> while reading PMI socket. MPI process died?
> TACC: MPI job exited with code: 1
>
> TACC: Shutdown complete. Exiting.
>
>
> NOTE 1 [file lnanopf3.top, line 4422]:
>   System has non-zero total charge: -0.018000
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
>
>
> ---
> Program grompp, VERSION 4.6.5
> Source code file:
> /work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line:
> 593
>
> File input/output error:
> /work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro
>
> ...
>
> Thanks a lot!
>
> regards
> Chetan
>
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[gmx-users] Simplified picture: comments invited

[Chetan Mahajan]

Hi,

Unfortunately, there is no scope I can try smaller version of the system.
However, let me explain one lead that I indicated earlier. Coulomb energy
at the end of minimization is -5E-7, which becomes "-nan" at the zeroth
step of NPT molecular dynamics run after minimization and thus code
crashes. Question is what is it that is giving two different energy values
 (-5E-7 and -nan) for the same atomic configurations ( end of minimization,
beginning of molecular dynamics)? I removed barostat, thermostat, h-bond
constraints from the MD code, so as to come as close to minimization run as
possible. However, coulomb energy in MD code is still blowing up. This is
very interesting since as I said we have two points with different energy,
but same atomic configuration, any further leads?

(total charge is -0.018 in both minimization as well as MD code, so that's
not affecting, water is flexible during minimization and not so during MD.
However, that should not matter, since code is crashing very initial step
of MD run).

Thanks
Chetan


On Sun, Jun 1, 2014 at 5:11 PM, Mark Abraham 
wrote:

> Hi,
>
> What's the smallest relevant neutral system you can think of? Test your
> implementation of your model on that, on a local machine, not a
> supercomputer ;-) If there's any diagnosis of why the crash happens, it
> will be in the log file. But you seem like you have far too many variables
> to know where the major problem lies.
>
> Mark
>
>
> On Sun, Jun 1, 2014 at 11:55 PM, Chetan Mahajan 
> wrote:
>
> > More information:
> >
> > As the log file shows, coulomb interaction energy is shooting to nan
> during
> > equilibration where error occurs. Coulomb interaction energy during
> > minimization is finite.
> >
> > Thanks
> > Chetan
> >
> >
> > On Sun, Jun 1, 2014 at 4:44 PM, Chetan Mahajan 
> > wrote:
> >
> > > Dear All,
> > >
> > > I am testing my gromacs code using user-specified potential functions
> (LJ
> > > as well as Buckingham as non-bonded potentials). *Minimization run with
> > > these potentials runs fine*. However, equilibration run gives following
> > > error at which I am clueless. Could anyone help? Is it because total
> > charge
> > > is -0.018 and not zero?
> > >
> > > ...
> > >
> > > Non-default thread affinity set probably by the OpenMP library,
> > > disabling internal thread affinity
> > > starting mdrun 'tio2_formate'
> > > 100 steps,   1000.0 ps.
> > > [c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler]
> Caught
> > > error: Segmentation fault (signal 11)
> > > [c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected
> > > End-Of-File on file descriptor 7. MPI process died?
> > > [c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error
> > > while reading PMI socket. MPI process died?
> > > [c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI
> > process
> > > (rank: 5, pid: 122921) terminated with signal 11 -> abort job
> > > [c418-701.stampede.tacc.utexas.edu:
> > mpirun_rsh][process_mpispawn_connection]
> > > mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket
> > (4)
> > > [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
> > > End-Of-File on file descriptor 21. MPI process died?
> > > [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected
> > > End-Of-File on file descriptor 21. MPI process died?
> > > [c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error
> > > while reading PMI socket. MPI process died?
> > > [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
> > > End-Of-File on file descriptor 21. MPI process died?
> > > [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected
> > > End-Of-File on file descriptor 21. MPI process died?
> > > [c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error
> > > while reading PMI socket. MPI process died?
> > > TACC: MPI job exited with code: 1
> > >
> > > TACC: Shutdown complete. Exiting.
> > >
> > >
> > > NOTE 1 [file lnanopf3.top, line 4422]:
> > >   System has non-zero total charge: -0.018000
> > >   Total charge should normally be an integer. See
> > >   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > >   for discussion on how close it should be to an integer.
> > >
> > >
> > >
> > >
> > > 

[gmx-users] peculiar water behavior

[Chetan Mahajan]

Dear All,

I am simulating TiO2 crystal solvated by water  and ions like sodium and
formate. I am observing one peculiar thing, and I would like to rectify
that. I have initial structure of crystal slab at the center of the box
elongated in z-direction and almost equal boxlength on both the sides, with
a gap of 1 nm between slab surface and first layer of water close to slab.
 This space is kept to avoid water going on the sides of the crystal during
equilibration. This was a minor information. Now, the main observation is
that during NPT equilibration, water from one side of the slab enters the
other opposite side of the slab (using periodic conditions) so that
boxlengths on both sides of the slab are very different at the end of
equilibration. Is this an artifact of pressure coupling? Following is my
equilibration .mdp file. I have tried varying the compressibility and tau-p
parameters in the following file. e.g. zero compressibility in x/y
direction or tau-p reduced to 3.
No success.

I look forward to hearing from you. I would ideally want water to not leave
the box.

Thanks
Chetan

title= NPTequilibration of  ligand_nanop-anatase-tio2
integrator   = md-vv
dt   = 0.001
nsteps   = 100
nstxout  = 1000
nstvout  = 1000
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1000
nstlist  = 1
ns-type  = grid
rlist= 1.0
vdwtype  = user
coulombtype  = pme
rcoulomb = 1.0
rvdw = 1.0
energygrps   = Ti OT OW c h5 o HW Na
energygrp-table  = Ti Ti OT OT Ti OT Ti OW OT c OT h5 OT o
tcoupl   = Berendsen
tc-grps  = System
tau-t= 0.1
ref-t= 300
Pcoupl   = Berendsen
pcoupltype   = semiisotropic
tau-p= 5.0 5.0
compressibility  = 4.5e-5 4.5e-5
ref-p= 1.0 1.0
refcoord-scaling = com
gen-vel  = yes
gen-temp = 300
gen-seed = 173529
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Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

One more important observation that I forgot to share:

With water moving from one side of the crystal slab to other side (through
periodic boundaries), crystal slab moves in the same direction (after
water) to fill the void in the box. I am using "com" refcoord-scaling.

Thanks
Chetan


On Thu, Jun 12, 2014 at 10:15 PM, Chetan Mahajan 
wrote:

> Dear All,
>
> I am simulating TiO2 crystal solvated by water  and ions like sodium and
> formate. I am observing one peculiar thing, and I would like to rectify
> that. I have initial structure of crystal slab at the center of the box
> elongated in z-direction and almost equal boxlength on both the sides, with
> a gap of 1 nm between slab surface and first layer of water close to slab.
>  This space is kept to avoid water going on the sides of the crystal during
> equilibration. This was a minor information. Now, the main observation is
> that during NPT equilibration, water from one side of the slab enters the
> other opposite side of the slab (using periodic conditions) so that
> boxlengths on both sides of the slab are very different at the end of
> equilibration. Is this an artifact of pressure coupling? Following is my
> equilibration .mdp file. I have tried varying the compressibility and tau-p
> parameters in the following file. e.g. zero compressibility in x/y
> direction or tau-p reduced to 3.
> No success.
>
> I look forward to hearing from you. I would ideally want water to not
> leave the box.
>
> Thanks
> Chetan
>
> title= NPTequilibration of  ligand_nanop-anatase-tio2
> integrator   = md-vv
> dt   = 0.001
> nsteps   = 100
> nstxout  = 1000
> nstvout  = 1000
> nstlog   = 1000
> nstenergy= 1000
> nstxtcout= 1000
> nstlist  = 1
> ns-type  = grid
> rlist= 1.0
> vdwtype  = user
> coulombtype  = pme
> rcoulomb = 1.0
> rvdw = 1.0
> energygrps   = Ti OT OW c h5 o HW Na
> energygrp-table  = Ti Ti OT OT Ti OT Ti OW OT c OT h5 OT o
> tcoupl   = Berendsen
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> Pcoupl   = Berendsen
> pcoupltype   = semiisotropic
> tau-p= 5.0 5.0
> compressibility  = 4.5e-5 4.5e-5
> ref-p= 1.0 1.0
> refcoord-scaling = com
> gen-vel  = yes
> gen-temp = 300
> gen-seed = 173529
>
>
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Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

Hi Justin,

I, actually, do not want to preserve any voids. Initial void that I
mentioned is supposed to be filled by water during equilibration and it
does so. However, problem is that some or major quantity of water moves out
from one side of the box to enter from the opposite side (obeying periodic
boundary conditions) and crystal slab moving following water movement. Thus
although initially there is almost equal amount of water on both sides of
the slab, we have more water on one side of the slab than the other side
after equilibration. In other words, length of the box on one side of the
slab is more than the other side after equilibration, although it is same
on both sides before equilibration. My dilemma is whether this is due to
pressure coupling or any gromacs thing or due to potentials (mixed
buckingham and LJ)?

Thanks
Chetan


On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul  wrote:

>
>
> On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
>
>> Dear All,
>>
>> I am simulating TiO2 crystal solvated by water  and ions like sodium and
>> formate. I am observing one peculiar thing, and I would like to rectify
>> that. I have initial structure of crystal slab at the center of the box
>> elongated in z-direction and almost equal boxlength on both the sides,
>> with
>> a gap of 1 nm between slab surface and first layer of water close to slab.
>>   This space is kept to avoid water going on the sides of the crystal
>> during
>> equilibration. This was a minor information. Now, the main observation is
>> that during NPT equilibration, water from one side of the slab enters the
>> other opposite side of the slab (using periodic conditions) so that
>> boxlengths on both sides of the slab are very different at the end of
>> equilibration. Is this an artifact of pressure coupling? Following is my
>> equilibration .mdp file. I have tried varying the compressibility and
>> tau-p
>> parameters in the following file. e.g. zero compressibility in x/y
>> direction or tau-p reduced to 3.
>>
>
> With pressure coupling, any voids present in the system will be
> compressed.  If you need to try to preserve some sort of vacuum layers, use
> NVT.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

Other main observation is that crystal slab following water, moving in the
same direction, *despite of position restraints (refcoord-scaling=com
option). *
Thanks
Chetan


On Fri, Jun 13, 2014 at 1:45 PM, Chetan Mahajan 
wrote:

> Hi Justin,
>
> I, actually, do not want to preserve any voids. Initial void that I
> mentioned is supposed to be filled by water during equilibration and it
> does so. However, problem is that some or major quantity of water moves out
> from one side of the box to enter from the opposite side (obeying periodic
> boundary conditions) and crystal slab moving following water movement. Thus
> although initially there is almost equal amount of water on both sides of
> the slab, we have more water on one side of the slab than the other side
> after equilibration. In other words, length of the box on one side of the
> slab is more than the other side after equilibration, although it is same
> on both sides before equilibration. My dilemma is whether this is due to
> pressure coupling or any gromacs thing or due to potentials (mixed
> buckingham and LJ)?
>
> Thanks
> Chetan
>
>
> On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
>>
>>> Dear All,
>>>
>>> I am simulating TiO2 crystal solvated by water  and ions like sodium and
>>> formate. I am observing one peculiar thing, and I would like to rectify
>>> that. I have initial structure of crystal slab at the center of the box
>>> elongated in z-direction and almost equal boxlength on both the sides,
>>> with
>>> a gap of 1 nm between slab surface and first layer of water close to
>>> slab.
>>>   This space is kept to avoid water going on the sides of the crystal
>>> during
>>> equilibration. This was a minor information. Now, the main observation is
>>> that during NPT equilibration, water from one side of the slab enters the
>>> other opposite side of the slab (using periodic conditions) so that
>>> boxlengths on both sides of the slab are very different at the end of
>>> equilibration. Is this an artifact of pressure coupling? Following is my
>>> equilibration .mdp file. I have tried varying the compressibility and
>>> tau-p
>>> parameters in the following file. e.g. zero compressibility in x/y
>>> direction or tau-p reduced to 3.
>>>
>>
>> With pressure coupling, any voids present in the system will be
>> compressed.  If you need to try to preserve some sort of vacuum layers, use
>> NVT.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

Thanks.

No, same things do not happen when it's a NVT simulation or no mixed
potentials. Also, with mixed potentials in NPT simulation, this things of
slab moving in one direction (thus following water movement) happens only
with -com option of refcoord-scaling, *not with -all option for
refcoord-scaling. *

I have a crystal slab with equal amount of water on both the sides. During
NPT equilibration (with refcoord-scaling option of -com, not -all), some
water on side side of the slab enters opposite side due to periodic
boundary conditions I have (say water on the right side of the slab,
crosses boundary of the box and enter the left side of the slab due to
periodic boundaries. Even crystal slab follows this water and move same
distance in the same direction of water movement. Following link shares
pictures of the solvated slab before and after equilibration:


https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa

I feel, this is not an error, but it is odd. Due to periodicity we have,
output of any calculations will remain the same.  Again, with -all option
for refcoord scaling, this movement of water and slab DOES NOT occur.

Thanks a lot!
regards
Chetan


On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham 
wrote:

> Hi,
>
> Repeating myself - simplify things! Do sane things happen with NVT? With no
> mixed potentials?
>
> Your words aren't making sense to me - you'll do much better with pictures,
> making sure you turn on your visualizer's option to show the periodic box.
>
> Mark
>
>
> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan 
> wrote:
>
> > Hi Justin,
> >
> > I, actually, do not want to preserve any voids. Initial void that I
> > mentioned is supposed to be filled by water during equilibration and it
> > does so. However, problem is that some or major quantity of water moves
> out
> > from one side of the box to enter from the opposite side (obeying
> periodic
> > boundary conditions) and crystal slab moving following water movement.
> Thus
> > although initially there is almost equal amount of water on both sides of
> > the slab, we have more water on one side of the slab than the other side
> > after equilibration. In other words, length of the box on one side of the
> > slab is more than the other side after equilibration, although it is same
> > on both sides before equilibration. My dilemma is whether this is due to
> > pressure coupling or any gromacs thing or due to potentials (mixed
> > buckingham and LJ)?
> >
> > Thanks
> > Chetan
> >
> >
> > On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
> > >
> > >> Dear All,
> > >>
> > >> I am simulating TiO2 crystal solvated by water  and ions like sodium
> and
> > >> formate. I am observing one peculiar thing, and I would like to
> rectify
> > >> that. I have initial structure of crystal slab at the center of the
> box
> > >> elongated in z-direction and almost equal boxlength on both the sides,
> > >> with
> > >> a gap of 1 nm between slab surface and first layer of water close to
> > slab.
> > >>   This space is kept to avoid water going on the sides of the crystal
> > >> during
> > >> equilibration. This was a minor information. Now, the main observation
> > is
> > >> that during NPT equilibration, water from one side of the slab enters
> > the
> > >> other opposite side of the slab (using periodic conditions) so that
> > >> boxlengths on both sides of the slab are very different at the end of
> > >> equilibration. Is this an artifact of pressure coupling? Following is
> my
> > >> equilibration .mdp file. I have tried varying the compressibility and
> > >> tau-p
> > >> parameters in the following file. e.g. zero compressibility in x/y
> > >> direction or tau-p reduced to 3.
> > >>
> > >
> > > With pressure coupling, any voids present in the system will be
> > > compressed.  If you need to try to preserve some sort of vacuum layers,
> > use
> > > NVT.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20

Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

The pics should be seen in the reverse order. Due to sorting by name,
"After equilibration" pic occurs first.


On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan 
wrote:

> Thanks.
>
> No, same things do not happen when it's a NVT simulation or no mixed
> potentials. Also, with mixed potentials in NPT simulation, this things of
> slab moving in one direction (thus following water movement) happens only
> with -com option of refcoord-scaling, *not with -all option for
> refcoord-scaling. *
>
> I have a crystal slab with equal amount of water on both the sides. During
> NPT equilibration (with refcoord-scaling option of -com, not -all), some
> water on side side of the slab enters opposite side due to periodic
> boundary conditions I have (say water on the right side of the slab,
> crosses boundary of the box and enter the left side of the slab due to
> periodic boundaries. Even crystal slab follows this water and move same
> distance in the same direction of water movement. Following link shares
> pictures of the solvated slab before and after equilibration:
>
>
> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
>
> I feel, this is not an error, but it is odd. Due to periodicity we have,
> output of any calculations will remain the same.  Again, with -all option
> for refcoord scaling, this movement of water and slab DOES NOT occur.
>
> Thanks a lot!
> regards
> Chetan
>
>
> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Repeating myself - simplify things! Do sane things happen with NVT? With
>> no
>> mixed potentials?
>>
>> Your words aren't making sense to me - you'll do much better with
>> pictures,
>> making sure you turn on your visualizer's option to show the periodic box.
>>
>> Mark
>>
>>
>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan 
>> wrote:
>>
>> > Hi Justin,
>> >
>> > I, actually, do not want to preserve any voids. Initial void that I
>> > mentioned is supposed to be filled by water during equilibration and it
>> > does so. However, problem is that some or major quantity of water moves
>> out
>> > from one side of the box to enter from the opposite side (obeying
>> periodic
>> > boundary conditions) and crystal slab moving following water movement.
>> Thus
>> > although initially there is almost equal amount of water on both sides
>> of
>> > the slab, we have more water on one side of the slab than the other side
>> > after equilibration. In other words, length of the box on one side of
>> the
>> > slab is more than the other side after equilibration, although it is
>> same
>> > on both sides before equilibration. My dilemma is whether this is due to
>> > pressure coupling or any gromacs thing or due to potentials (mixed
>> > buckingham and LJ)?
>> >
>> > Thanks
>> > Chetan
>> >
>> >
>> > On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul  wrote:
>> >
>> > >
>> > >
>> > > On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
>> > >
>> > >> Dear All,
>> > >>
>> > >> I am simulating TiO2 crystal solvated by water  and ions like sodium
>> and
>> > >> formate. I am observing one peculiar thing, and I would like to
>> rectify
>> > >> that. I have initial structure of crystal slab at the center of the
>> box
>> > >> elongated in z-direction and almost equal boxlength on both the
>> sides,
>> > >> with
>> > >> a gap of 1 nm between slab surface and first layer of water close to
>> > slab.
>> > >>   This space is kept to avoid water going on the sides of the crystal
>> > >> during
>> > >> equilibration. This was a minor information. Now, the main
>> observation
>> > is
>> > >> that during NPT equilibration, water from one side of the slab enters
>> > the
>> > >> other opposite side of the slab (using periodic conditions) so that
>> > >> boxlengths on both sides of the slab are very different at the end of
>> > >> equilibration. Is this an artifact of pressure coupling? Following
>> is my
>> > >> equilibration .mdp file. I have tried varying the compressibility and
>> > >> tau-p
>> > >> parameters in the following file. e.g. zero compressibility in x/y
>> > >> direction or tau-p reduced to 3.
>> > >>
>> > >
>&g

Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

Any ideas :

1. why slab is moving despite of position constraints?

2. That too, only with "com" option of refcoord scaling...with "all" option
slab does not move...

Thanks


On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan 
wrote:

> The pics should be seen in the reverse order. Due to sorting by name,
> "After equilibration" pic occurs first.
>
>
> On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan 
> wrote:
>
>> Thanks.
>>
>> No, same things do not happen when it's a NVT simulation or no mixed
>> potentials. Also, with mixed potentials in NPT simulation, this things of
>> slab moving in one direction (thus following water movement) happens only
>> with -com option of refcoord-scaling, *not with -all option for
>> refcoord-scaling. *
>>
>> I have a crystal slab with equal amount of water on both the sides.
>> During NPT equilibration (with refcoord-scaling option of -com, not -all),
>> some water on side side of the slab enters opposite side due to periodic
>> boundary conditions I have (say water on the right side of the slab,
>> crosses boundary of the box and enter the left side of the slab due to
>> periodic boundaries. Even crystal slab follows this water and move same
>> distance in the same direction of water movement. Following link shares
>> pictures of the solvated slab before and after equilibration:
>>
>>
>> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
>>
>> I feel, this is not an error, but it is odd. Due to periodicity we have,
>> output of any calculations will remain the same.  Again, with -all option
>> for refcoord scaling, this movement of water and slab DOES NOT occur.
>>
>> Thanks a lot!
>> regards
>> Chetan
>>
>>
>> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham 
>> wrote:
>>
>>> Hi,
>>>
>>> Repeating myself - simplify things! Do sane things happen with NVT? With
>>> no
>>> mixed potentials?
>>>
>>> Your words aren't making sense to me - you'll do much better with
>>> pictures,
>>> making sure you turn on your visualizer's option to show the periodic
>>> box.
>>>
>>> Mark
>>>
>>>
>>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan 
>>> wrote:
>>>
>>> > Hi Justin,
>>> >
>>> > I, actually, do not want to preserve any voids. Initial void that I
>>> > mentioned is supposed to be filled by water during equilibration and it
>>> > does so. However, problem is that some or major quantity of water
>>> moves out
>>> > from one side of the box to enter from the opposite side (obeying
>>> periodic
>>> > boundary conditions) and crystal slab moving following water movement.
>>> Thus
>>> > although initially there is almost equal amount of water on both sides
>>> of
>>> > the slab, we have more water on one side of the slab than the other
>>> side
>>> > after equilibration. In other words, length of the box on one side of
>>> the
>>> > slab is more than the other side after equilibration, although it is
>>> same
>>> > on both sides before equilibration. My dilemma is whether this is due
>>> to
>>> > pressure coupling or any gromacs thing or due to potentials (mixed
>>> > buckingham and LJ)?
>>> >
>>> > Thanks
>>> > Chetan
>>> >
>>> >
>>> > On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul 
>>> wrote:
>>> >
>>> > >
>>> > >
>>> > > On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
>>> > >
>>> > >> Dear All,
>>> > >>
>>> > >> I am simulating TiO2 crystal solvated by water  and ions like
>>> sodium and
>>> > >> formate. I am observing one peculiar thing, and I would like to
>>> rectify
>>> > >> that. I have initial structure of crystal slab at the center of the
>>> box
>>> > >> elongated in z-direction and almost equal boxlength on both the
>>> sides,
>>> > >> with
>>> > >> a gap of 1 nm between slab surface and first layer of water close to
>>> > slab.
>>> > >>   This space is kept to avoid water going on the sides of the
>>> crystal
>>> > >> during
>>> > >> equilibration. This was a minor information. Now, the main
>>> observatio

Re: [gmx-users] peculiar water behavior

[Chetan Mahajan]

Thanks, Justin. That makes it clear. I have one small question: I do not
know how does position restraint algorithm work with other things in
gromacs, but  doesn't it generate a lot of stress due to slab moving from
center to near box boundary despite of position restraints, when -com
option is used for refcoord-scaling? If there is a lot of stress, would
this stress affect simulation results?

Thanks and Regards,
Chetan


On Tue, Jun 17, 2014 at 10:01 AM, Justin Lemkul  wrote:

>
>
> On 6/17/14, 10:32 AM, Chetan Mahajan wrote:
>
>> Any ideas :
>>
>> 1. why slab is moving despite of position constraints?
>>
>>
> Restraints are biasing potentials; they don't prevent movement.  Why is it
> necessary that your slab not move?
>
>
>  2. That too, only with "com" option of refcoord scaling...with "all"
>> option
>> slab does not move...
>>
>>
> Using "all" means the restraint reference for each atom is the original
> position in the input coordinates, with respect to every atom individually.
>  It is more stringent, though it can often be unstable.  The "com" option
> means the restraint potential is calculated with respect to the COM of the
> group of restrained atoms; it is a bit more forgiving, since the COM might
> only move slightly, even if there are relatively larger changes in the
> individual atomic positions.
>
> -Justin
>
>  Thanks
>>
>>
>> On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan 
>> wrote:
>>
>>  The pics should be seen in the reverse order. Due to sorting by name,
>>> "After equilibration" pic occurs first.
>>>
>>>
>>> On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan 
>>> wrote:
>>>
>>>  Thanks.
>>>>
>>>> No, same things do not happen when it's a NVT simulation or no mixed
>>>> potentials. Also, with mixed potentials in NPT simulation, this things
>>>> of
>>>> slab moving in one direction (thus following water movement) happens
>>>> only
>>>> with -com option of refcoord-scaling, *not with -all option for
>>>> refcoord-scaling. *
>>>>
>>>>
>>>> I have a crystal slab with equal amount of water on both the sides.
>>>> During NPT equilibration (with refcoord-scaling option of -com, not
>>>> -all),
>>>> some water on side side of the slab enters opposite side due to periodic
>>>> boundary conditions I have (say water on the right side of the slab,
>>>> crosses boundary of the box and enter the left side of the slab due to
>>>> periodic boundaries. Even crystal slab follows this water and move same
>>>> distance in the same direction of water movement. Following link shares
>>>> pictures of the solvated slab before and after equilibration:
>>>>
>>>>
>>>> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
>>>>
>>>> I feel, this is not an error, but it is odd. Due to periodicity we have,
>>>> output of any calculations will remain the same.  Again, with -all
>>>> option
>>>> for refcoord scaling, this movement of water and slab DOES NOT occur.
>>>>
>>>> Thanks a lot!
>>>> regards
>>>> Chetan
>>>>
>>>>
>>>> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham >>> >
>>>> wrote:
>>>>
>>>>  Hi,
>>>>>
>>>>> Repeating myself - simplify things! Do sane things happen with NVT?
>>>>> With
>>>>> no
>>>>> mixed potentials?
>>>>>
>>>>> Your words aren't making sense to me - you'll do much better with
>>>>> pictures,
>>>>> making sure you turn on your visualizer's option to show the periodic
>>>>> box.
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan 
>>>>> wrote:
>>>>>
>>>>>  Hi Justin,
>>>>>>
>>>>>> I, actually, do not want to preserve any voids. Initial void that I
>>>>>> mentioned is supposed to be filled by water during equilibration and
>>>>>> it
>>>>>> does so. However, problem is that some or major quantity of water
>>>>>>
>>>>> moves out
>>>>>
>>>>>> from one side of the box to enter f