Re: [gmx-users] Test Particle Insertion

[João M . Damas]

Dear Anh,

You need to construct a .tpr file for the mdrun -rerun with:

   - a .gro file with the ligand to be inserted at the end, which _must_ be
   geometrically centered at 0,0,0 ;
   - a matching .top file (which means with the ligand topology
   appropriately inserted) ;
   - a .mdp file with the specific parameters for the tpi algorithm .

Since you happen to have a single particle to insert, that particle's
coordinates should be 0,0,0 in the .gro file from grompp (your initial.gro).

Best,
João


On Thu, Jun 20, 2013 at 8:08 PM, Phan, Anh T.  wrote:

> Dear GMX Users,
> My name is Anh Phan, a PhD student at University of Oklahoma.
> I would like to calculate excess chemical potential of one gas molecule in
> water solvent using Widom test particle insertion with Gromacs.
> In this method, I will insert this gas molecule at a random position in
> each configuration of the system.
> With Gromacs, I see I can use tpi (integrator = tpi).
> I know I have to add this gas molecule in the topology (topol.top)
> Also, it is indicated in the manual that insertions are performed nsteps
> times in each frame at random locations and with random orientiations of
> the molecule. That is what I desire.
> The question I would like to ask is whether I have to add the specified
> coordinate of gas molecule in the .gro file at the beginning of running
> simulation.
> For example, in the initial.gro file
> .
> 26734SOL OW45744  21.969   6.237   2.921
> 26734SOLHW145745  21.969   6.253   3.019
> 26734SOLHW245746  21.886   6.188   2.895
> 26735SOL OW45747  15.155   7.211   2.853
> 26735SOLHW145748  15.220   7.265   2.801
> 26735SOLHW245749  15.204   7.151   2.916
> 26736SOL OW45750  24.606   4.896   3.053
> 26736SOLHW145751  24.594   4.972   2.989
> 26736SOLHW245752  24.532   4.896   3.120
> 26737INS X457521.0001.0001.000 ( Do I
> have to add this line in the initial.gro file)
>
> The command lines
> grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr
> -maxwarn 2
> mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g
> init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg
>
> I am looking forward to receiving your reply.
> Thank you for your help.
> Sincerely,
> Anh
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [gmx-users] Test Particle Insertion

[Naga Rajesh Tummala]

As far as I know it should not be included. Make a tpr file new .top and
input file and run the mdrun with -rerun option as described here.  "
http://manual.gromacs.org/online/mdp_opt.html#run";


Cheers,
Rajesh

On Thu, Jun 20, 2013 at 3:08 PM, Phan, Anh T.  wrote:

> Dear GMX Users,
> My name is Anh Phan, a PhD student at University of Oklahoma.
> I would like to calculate excess chemical potential of one gas molecule in
> water solvent using Widom test particle insertion with Gromacs.
> In this method, I will insert this gas molecule at a random position in
> each configuration of the system.
> With Gromacs, I see I can use tpi (integrator = tpi).
> I know I have to add this gas molecule in the topology (topol.top)
> Also, it is indicated in the manual that insertions are performed nsteps
> times in each frame at random locations and with random orientiations of
> the molecule. That is what I desire.
> The question I would like to ask is whether I have to add the specified
> coordinate of gas molecule in the .gro file at the beginning of running
> simulation.
> For example, in the initial.gro file
> .
> 26734SOL OW45744  21.969   6.237   2.921
> 26734SOLHW145745  21.969   6.253   3.019
> 26734SOLHW245746  21.886   6.188   2.895
> 26735SOL OW45747  15.155   7.211   2.853
> 26735SOLHW145748  15.220   7.265   2.801
> 26735SOLHW245749  15.204   7.151   2.916
> 26736SOL OW45750  24.606   4.896   3.053
> 26736SOLHW145751  24.594   4.972   2.989
> 26736SOLHW245752  24.532   4.896   3.120
> 26737INS X457521.0001.0001.000 ( Do I
> have to add this line in the initial.gro file)
>
> The command lines
> grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr
> -maxwarn 2
> mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g
> init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg
>
> I am looking forward to receiving your reply.
> Thank you for your help.
> Sincerely,
> Anh
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Naga Rajesh Tummala, PhD
Post-Doctoral Researcher,
School of Chemistry and Biochemistry,
Georgia Institute of Technology
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[gmx-users] Test Particle Insertion

[Phan, Anh T.]

Dear GMX Users,
My name is Anh Phan, a PhD student at University of Oklahoma.
I would like to calculate excess chemical potential of one gas molecule in 
water solvent using Widom test particle insertion with Gromacs.
In this method, I will insert this gas molecule at a random position in each 
configuration of the system.
With Gromacs, I see I can use tpi (integrator = tpi).
I know I have to add this gas molecule in the topology (topol.top)
Also, it is indicated in the manual that insertions are performed nsteps times 
in each frame at random locations and with random orientiations of the 
molecule. That is what I desire.
The question I would like to ask is whether I have to add the specified 
coordinate of gas molecule in the .gro file at the beginning of running 
simulation.
For example, in the initial.gro file
.
26734SOL OW45744  21.969   6.237   2.921
26734SOLHW145745  21.969   6.253   3.019
26734SOLHW245746  21.886   6.188   2.895
26735SOL OW45747  15.155   7.211   2.853
26735SOLHW145748  15.220   7.265   2.801
26735SOLHW245749  15.204   7.151   2.916
26736SOL OW45750  24.606   4.896   3.053
26736SOLHW145751  24.594   4.972   2.989
26736SOLHW245752  24.532   4.896   3.120
26737INS X457521.0001.0001.000 ( Do I have 
to add this line in the initial.gro file)

The command lines
grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr 
-maxwarn 2
mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g 
init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg

I am looking forward to receiving your reply.
Thank you for your help.
Sincerely,
Anh
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[gmx-users] test, please ignore

[Rossen Apostolov]

test
*test*
/test/
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Re: [gmx-users] Test Particle Insertion

[Javier Cerezo]

Hi

Well, according to the link you pointed out, the Widom technique gives 
you the excess chemical potential, as we discussed. mu and mu_ideal (in 
your link) are not calculated, those are just the reference states 
between which the Widom technique calculates the excess chem pot.


As I said, I think U_{n+1} refers to the interaction energy of the 
inserte particle with the system, but maybe someone could confirm or 
correct.


Javier

El 16/05/12 11:44, Steven Neumann escribió:



On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo > wrote:


About the red curve, I guess fluctuations might be directly
related to volume fluctuations, you can extract the volume over
time from g_energy (boxXX*boxYY**boxZZ) and compare. (just another
comment, now I am not very sure about the "f." that precedes the
red line legend..)

About the interpretation of the quantities, the Widom technique
does not provide you with an absolute value of the chemical
potential but directly with the excess chemical potential. So,
mu=-kTlog(Ve ^ (U*B)/(V))n+1 is the excess chemical potential,
where (if I recall correctly) U_{n+1} is the the interaction
energy  between the inserted particle and the rest of the system.
You don't need (and should not do) such post-processing operations
that you proposed to get the excess chemical potential.

Javier


Thank you.
In this case I am considering the curve with NPT - with volume.

From the equation u=-kTlog(Ve ^ (U*B)/(V))n+1  (the one on the plot - 
if it is correct! Or it should be with delta?) we will obtain the 
chemical potential of the system with N+1 molecules. To obtain the 
excess we need to have chemical potential of the system wit N 
particles and the substract it according to the 
equation:http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method
If it is a mistake and there is deltaU this is the exceess, if not 
this is only for N+1. Please, correct me if I am wrong.


Steven



El 16/05/12 11:06, Steven Neumann escribió:

Thank you very much! I just saw your response.

As I run it in NPT ensemble the plot with volume is important for
me. Please, See the plot:

http://speedy.sh/CJn5b/tpiN.jpg

So does the fluctuating red curve make any sesnse then if it does
not consider volume?

Another thing: this is chemical potential of the system with
extra water molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1?
So if I want to obtain the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the
system with N molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my
previosu system and calculate the total potential energy then
-kTlog... of this values and then substract it? Please correct me
if I am wrong.

Steven


On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo mailto:j...@um.es>> wrote:

Hi Steven.



1. Why this value is divided by nm3? Shall I multiply it by
the simulation box?

It is not not divided by nm3. The legend for "y" axis is not
appropriate for your plot. Keep in mind that the same graph
is used to represent lots of quantities (you can plot all of
them with xmgrace -nxy tpi.xvg). The "y" axis is not the same
for all, but only one label is possible, so developers have
to chose which label to place on the axis. But this is just a
label, don't give much importance to it and analyse you
results (including units) according to the equations and the
standard units in gromacs.


2. Why e^(-BU) is multiplied by V? I just want to have the
excess chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how
can I get deltaU?

The volume appears in the expression of the excess chemical
potential if you are running a NpT ensemble. The second plot
(if you use xmgrace -nxy tpi.xvg) does not contain the volume.


3. The value corresponds to the plateau so I should run it
for longer time?

You are getting a time&ensemble average and for large
sampling (and large simulation times), this average should
converge. So, the final value you will get is the last point
of the graph, it up to you to say if it is converged. So you
can try to enlarge the number of points sampled, if the shape
does not change you are sampling correctly every snapshot,
then take longer simulation times if you want to converge
your results.

Javier


El 15/05/12 09:57, Steven Neumann escribió:



On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>> wrote:



On 5/14/12 11:53 AM, Steven Neumann wrote:

Dear Gmx Users,

Did anyone use TPI method for the calculation of
chemical potential? 

Re: [gmx-users] Test Particle Insertion

[Steven Neumann]

On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo  wrote:

>  About the red curve, I guess fluctuations might be directly related to
> volume fluctuations, you can extract the volume over time from g_energy
> (boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not very
> sure about the "f." that precedes the red line legend..)
>
> About the interpretation of the quantities, the Widom technique does not
> provide you with an absolute value of the chemical potential but directly
> with the excess chemical potential. So, mu=-kTlog(Ve ^ (U*B)/(V))n+1 is the
> excess chemical potential, where (if I recall correctly) U_{n+1} is the the
> interaction energy  between the inserted particle and the rest of the
> system. You don't need (and should not do) such post-processing operations
> that you proposed to get the excess chemical potential.
>
> Javier
>

Thank you.
In this case I am considering the curve with NPT - with volume.

>From the equation u=-kTlog(Ve ^ (U*B)/(V))n+1  (the one on the plot - if it
is correct! Or it should be with delta?) we will obtain the chemical
potential of the system with N+1 molecules. To obtain the excess we need to
have chemical potential of the system wit N particles and the substract it
according to the equation:
http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method
If it is a mistake and there is deltaU this is the exceess, if not this is
only for N+1. Please, correct me if I am wrong.

Steven


>
>
> El 16/05/12 11:06, Steven Neumann escribió:
>
> Thank you very much! I just saw your response.
>
> As I run it in NPT ensemble the plot with volume is important for me.
> Please, See the plot:
>
> http://speedy.sh/CJn5b/tpiN.jpg
>
> So does the fluctuating red curve make any sesnse then if it does not
> consider volume?
>
> Another thing: this is chemical potential of the system with extra water
> molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want to obtain
> the excess chemical potential:
> u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system with N
> molecules and then substract it.
> Is it calculated somewhere or I should use g_energy of my previosu system
> and calculate the total potential energy then -kTlog... of this values and
> then substract it? Please correct me if I am wrong.
>
> Steven
>
>
> On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo  wrote:
>
>>  Hi Steven.
>>
>>
>>
>>  1. Why this value is divided by nm3? Shall I multiply it by the
>> simulation box?
>>
>>  It is not not divided by nm3. The legend for "y" axis is not appropriate
>> for your plot. Keep in mind that the same graph is used to represent lots
>> of quantities (you can plot all of them with xmgrace -nxy tpi.xvg). The "y"
>> axis is not the same for all, but only one label is possible, so developers
>> have to chose which label to place on the axis. But this is just a label,
>> don't give much importance to it and analyse you results (including units)
>> according to the equations and the standard units in gromacs.
>>
>>  2. Why e^(-BU) is multiplied by V? I just want to have the excess
>> chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
>>
>>  The volume appears in the expression of the excess chemical potential if
>> you are running a NpT ensemble. The second plot (if you use xmgrace -nxy
>> tpi.xvg) does not contain the volume.
>>
>>   3. The value corresponds to the plateau so I should run it for longer
>> time?
>>
>>  You are getting a time&ensemble average and for large sampling (and
>> large simulation times), this average should converge. So, the final value
>> you will get is the last point of the graph, it up to you to say if it is
>> converged. So you can try to enlarge the number of points sampled, if the
>> shape does not change you are sampling correctly every snapshot, then take
>> longer simulation times if you want to converge your results.
>>
>> Javier
>>
>>
>> El 15/05/12 09:57, Steven Neumann escribió:
>>
>>
>>
>> On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul wrote:
>>
>>>
>>>
>>> On 5/14/12 11:53 AM, Steven Neumann wrote:
>>>
 Dear Gmx Users,

 Did anyone use TPI method for the calculation of chemical potential?
 The tpi.xvg
 files consists of:

 @ s0 legend "-kT log(/)"
 @ s1 legend "f. -kT log"
 @ s2 legend "f. "
 @ s3 legend "f. V"
 @ s4 legend "f. "
 @ s5 legend "f. "
 @ s6 legend "f. "
 @ s7 legend "f. "
 @ s8 legend "f. "

 @xaxis  label "Time (ps)"
 @yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"

 Can anyone explain me these legends? I just want obtain a value of the
 excess
 chemical potential according to the equation:
 u=-kT log (-deltaV/kT), Which legend is responsible for this and what
 are the
 units? kJ/mol? Please, explain as the above letters does not mean to me
 anything?


>>>  These strings are formatted for XmGrace.  Have you tried plotting the
>>> file to see what

Re: [gmx-users] Test Particle Insertion

[Javier Cerezo]

About the red curve, I guess fluctuations might be directly related to 
volume fluctuations, you can extract the volume over time from g_energy 
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not 
very sure about the "f." that precedes the red line legend..)


About the interpretation of the quantities, the Widom technique does not 
provide you with an absolute value of the chemical potential but 
directly with the excess chemical potential. So, mu=-kTlog(Ve ^ 
(U*B)/(V))n+1 is the excess chemical potential, where (if I recall 
correctly) U_{n+1} is the the interaction energy  between the inserted 
particle and the rest of the system. You don't need (and should not do) 
such post-processing operations that you proposed to get the excess 
chemical potential.


Javier


El 16/05/12 11:06, Steven Neumann escribió:

Thank you very much! I just saw your response.

As I run it in NPT ensemble the plot with volume is important for me. 
Please, See the plot:


http://speedy.sh/CJn5b/tpiN.jpg

So does the fluctuating red curve make any sesnse then if it does not 
consider volume?


Another thing: this is chemical potential of the system with extra 
water molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want 
to obtain the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system 
with N molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my previosu 
system and calculate the total potential energy then -kTlog... of this 
values and then substract it? Please correct me if I am wrong.


Steven


On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo > wrote:


Hi Steven.



1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?

It is not not divided by nm3. The legend for "y" axis is not
appropriate for your plot. Keep in mind that the same graph is
used to represent lots of quantities (you can plot all of them
with xmgrace -nxy tpi.xvg). The "y" axis is not the same for all,
but only one label is possible, so developers have to chose which
label to place on the axis. But this is just a label, don't give
much importance to it and analyse you results (including units)
according to the equations and the standard units in gromacs.


2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get
deltaU?

The volume appears in the expression of the excess chemical
potential if you are running a NpT ensemble. The second plot (if
you use xmgrace -nxy tpi.xvg) does not contain the volume.


3. The value corresponds to the plateau so I should run it for
longer time?

You are getting a time&ensemble average and for large sampling
(and large simulation times), this average should converge. So,
the final value you will get is the last point of the graph, it up
to you to say if it is converged. So you can try to enlarge the
number of points sampled, if the shape does not change you are
sampling correctly every snapshot, then take longer simulation
times if you want to converge your results.

Javier


El 15/05/12 09:57, Steven Neumann escribió:



On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>> wrote:



On 5/14/12 11:53 AM, Steven Neumann wrote:

Dear Gmx Users,

Did anyone use TPI method for the calculation of chemical
potential? The tpi.xvg
files consists of:

@ s0 legend "-kT log(/)"
@ s1 legend "f. -kT log"
@ s2 legend "f. "
@ s3 legend "f. V"
@ s4 legend "f. "
@ s5 legend "f. "
@ s6 legend "f. "
@ s7 legend "f. "
@ s8 legend "f. "

@xaxis  label "Time (ps)"
@yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"

Can anyone explain me these legends? I just want obtain a
value of the excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for
this and what are the
units? kJ/mol? Please, explain as the above letters does
not mean to me anything?


These strings are formatted for XmGrace.  Have you tried
plotting the file to see what it contains?  The legends will
be far more obvious if you do.

-Justin


Thank you Justin.
Can anyone explain me from the plot:

http://speedy.sh/Xpnws/tpi.JPG

1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get
deltaU?
3. The value corresponds to the plateau so I should run it for
longer time?


Thank you,

 

Re: [gmx-users] Test Particle Insertion

[Steven Neumann]

Thank you very much! I just saw your response.

As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:

http://speedy.sh/CJn5b/tpiN.jpg

So does the fluctuating red curve make any sesnse then if it does not
consider volume?

Another thing: this is chemical potential of the system with extra water
molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want to obtain
the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system with N
molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my previosu system
and calculate the total potential energy then -kTlog... of this values and
then substract it? Please correct me if I am wrong.

Steven


On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo  wrote:

>  Hi Steven.
>
>
>
>  1. Why this value is divided by nm3? Shall I multiply it by the
> simulation box?
>
> It is not not divided by nm3. The legend for "y" axis is not appropriate
> for your plot. Keep in mind that the same graph is used to represent lots
> of quantities (you can plot all of them with xmgrace -nxy tpi.xvg). The "y"
> axis is not the same for all, but only one label is possible, so developers
> have to chose which label to place on the axis. But this is just a label,
> don't give much importance to it and analyse you results (including units)
> according to the equations and the standard units in gromacs.
>
>  2. Why e^(-BU) is multiplied by V? I just want to have the excess
> chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
>
> The volume appears in the expression of the excess chemical potential if
> you are running a NpT ensemble. The second plot (if you use xmgrace -nxy
> tpi.xvg) does not contain the volume.
>
>   3. The value corresponds to the plateau so I should run it for longer
> time?
>
> You are getting a time&ensemble average and for large sampling (and large
> simulation times), this average should converge. So, the final value you
> will get is the last point of the graph, it up to you to say if it is
> converged. So you can try to enlarge the number of points sampled, if the
> shape does not change you are sampling correctly every snapshot, then take
> longer simulation times if you want to converge your results.
>
> Javier
>
>
> El 15/05/12 09:57, Steven Neumann escribió:
>
>
>
> On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> On 5/14/12 11:53 AM, Steven Neumann wrote:
>>
>>> Dear Gmx Users,
>>>
>>> Did anyone use TPI method for the calculation of chemical potential? The
>>> tpi.xvg
>>> files consists of:
>>>
>>> @ s0 legend "-kT log(/)"
>>> @ s1 legend "f. -kT log"
>>> @ s2 legend "f. "
>>> @ s3 legend "f. V"
>>> @ s4 legend "f. "
>>> @ s5 legend "f. "
>>> @ s6 legend "f. "
>>> @ s7 legend "f. "
>>> @ s8 legend "f. "
>>>
>>> @xaxis  label "Time (ps)"
>>> @yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"
>>>
>>> Can anyone explain me these legends? I just want obtain a value of the
>>> excess
>>> chemical potential according to the equation:
>>> u=-kT log (-deltaV/kT), Which legend is responsible for this and what
>>> are the
>>> units? kJ/mol? Please, explain as the above letters does not mean to me
>>> anything?
>>>
>>>
>>  These strings are formatted for XmGrace.  Have you tried plotting the
>> file to see what it contains?  The legends will be far more obvious if you
>> do.
>>
>> -Justin
>>
>
> Thank you Justin.
> Can anyone explain me from the plot:
>
> http://speedy.sh/Xpnws/tpi.JPG
>
> 1. Why this value is divided by nm3? Shall I multiply it by the simulation
> box?
> 2. Why e^(-BU) is multiplied by V? I just want to have the excess chemical
> potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
> 3. The value corresponds to the plateau so I should run it for longer time?
>
>
> Thank you,
>
> Steven
>
>
>>
>> --
>> 
>>
>> Justin A. Lemkul, Ph.D.
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interfa

Re: [gmx-users] Test Particle Insertion

[Steven Neumann]

On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul  wrote:

>
>
> On 5/14/12 11:53 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> Did anyone use TPI method for the calculation of chemical potential? The
>> tpi.xvg
>> files consists of:
>>
>> @ s0 legend "-kT log(/)"
>> @ s1 legend "f. -kT log"
>> @ s2 legend "f. "
>> @ s3 legend "f. V"
>> @ s4 legend "f. "
>> @ s5 legend "f. "
>> @ s6 legend "f. "
>> @ s7 legend "f. "
>> @ s8 legend "f. "
>>
>> @xaxis  label "Time (ps)"
>> @yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"
>>
>> Can anyone explain me these legends? I just want obtain a value of the
>> excess
>> chemical potential according to the equation:
>> u=-kT log (-deltaV/kT), Which legend is responsible for this and what are
>> the
>> units? kJ/mol? Please, explain as the above letters does not mean to me
>> anything?
>>
>>
> These strings are formatted for XmGrace.  Have you tried plotting the file
> to see what it contains?  The legends will be far more obvious if you do.
>
> -Justin
>

Thank you Justin.
Can anyone explain me from the plot:

http://speedy.sh/Xpnws/tpi.JPG

1. Why this value is divided by nm3? Shall I multiply it by the simulation
box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess chemical
potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
3. The value corresponds to the plateau so I should run it for longer time?


Thank you,

Steven


>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
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Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Test Particle Insertion

[Javier Cerezo]

Hi Steven.

1. Why this value is divided by nm3? Shall I multiply it by the 
simulation box?
It is not not divided by nm3. The legend for "y" axis is not appropriate 
for your plot. Keep in mind that the same graph is used to represent 
lots of quantities (you can plot all of them with xmgrace -nxy tpi.xvg). 
The "y" axis is not the same for all, but only one label is possible, so 
developers have to chose which label to place on the axis. But this is 
just a label, don't give much importance to it and analyse you results 
(including units) according to the equations and the standard units in 
gromacs.
2. Why e^(-BU) is multiplied by V? I just want to have the excess 
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
The volume appears in the expression of the excess chemical potential if 
you are running a NpT ensemble. The second plot (if you use xmgrace -nxy 
tpi.xvg) does not contain the volume.
3. The value corresponds to the plateau so I should run it for longer 
time?
You are getting a time&ensemble average and for large sampling (and 
large simulation times), this average should converge. So, the final 
value you will get is the last point of the graph, it up to you to say 
if it is converged. So you can try to enlarge the number of points 
sampled, if the shape does not change you are sampling correctly every 
snapshot, then take longer simulation times if you want to converge your 
results.


Javier


El 15/05/12 09:57, Steven Neumann escribió:



On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul > wrote:




On 5/14/12 11:53 AM, Steven Neumann wrote:

Dear Gmx Users,

Did anyone use TPI method for the calculation of chemical
potential? The tpi.xvg
files consists of:

@ s0 legend "-kT log(/)"
@ s1 legend "f. -kT log"
@ s2 legend "f. "
@ s3 legend "f. V"
@ s4 legend "f. "
@ s5 legend "f. "
@ s6 legend "f. "
@ s7 legend "f. "
@ s8 legend "f. "

@xaxis  label "Time (ps)"
@yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"

Can anyone explain me these legends? I just want obtain a
value of the excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this
and what are the
units? kJ/mol? Please, explain as the above letters does not
mean to me anything?


These strings are formatted for XmGrace.  Have you tried plotting
the file to see what it contains?  The legends will be far more
obvious if you do.

-Justin


Thank you Justin.
Can anyone explain me from the plot:

http://speedy.sh/Xpnws/tpi.JPG

1. Why this value is divided by nm3? Shall I multiply it by the 
simulation box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess 
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
3. The value corresponds to the plateau so I should run it for longer 
time?



Thank you,

Steven


-- 



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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interface or send it to gmx-users-requ...@gromacs.org
.
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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Test Particle Insertion

[Justin A. Lemkul]

On 5/14/12 11:53 AM, Steven Neumann wrote:

Dear Gmx Users,

Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg
files consists of:

@ s0 legend "-kT log(/)"
@ s1 legend "f. -kT log"
@ s2 legend "f. "
@ s3 legend "f. V"
@ s4 legend "f. "
@ s5 legend "f. "
@ s6 legend "f. "
@ s7 legend "f. "
@ s8 legend "f. "

@xaxis  label "Time (ps)"
@yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"

Can anyone explain me these legends? I just want obtain a value of the excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this and what are the
units? kJ/mol? Please, explain as the above letters does not mean to me 
anything?



These strings are formatted for XmGrace.  Have you tried plotting the file to 
see what it contains?  The legends will be far more obvious if you do.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Test Particle Insertion

[Steven Neumann]

Dear Gmx Users,

Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg files consists of:

@ s0 legend "-kT log(/)"
@ s1 legend "f. -kT log"
@ s2 legend "f. "
@ s3 legend "f. V"
@ s4 legend "f. "
@ s5 legend "f. "
@ s6 legend "f. "
@ s7 legend "f. "
@ s8 legend "f. "

@xaxis  label "Time (ps)"
@yaxis  label "(kJ mol\S-1\N) / (nm\S3\N)"

Can anyone explain me these legends? I just want obtain a value of the
excess chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this and what are
the units? kJ/mol? Please, explain as the above letters does not mean to me
anything?

Thank you,

Steven
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] Test Particle Insertion of Water

[Steven Neumann]

Thank you! I have missed it somehow. I can still use my xtc trajectory.

Steven

On Wed, May 9, 2012 at 3:16 PM, Javier Cerezo  wrote:

>  The trr file has something wrong. Look at "Coords", it has 0 frames
>
> You may have forgotten to set nstxout to a non-zero value?
>
> Javier
>
> El 09/05/12 16:10, Steven Neumann escribió:
>
> I added one water molecule in my topology to all water molecules:
>
> [ molecules ]
> ; Compound#mols
> Alanine40
> SOL   724
>
> Maybe I should add aditional line like:
>
> [ molecules ]
> ; Compound#mols
> Alanine40
> SOL   723
> SOL  1
>
> What do you think?
>
>
> On Wed, May 9, 2012 at 3:04 PM, Steven Neumann wrote:
>
>> Checking file md.trr
>> trn version: GMX_trn_file (single precision)
>> Reading frame   0 time0.000
>> # Atoms  2569
>> Last frame   2000 time 10.000
>>
>>
>> Item#frames Timestep (ps)
>> Step  200150
>> Time  200150
>> Lambda200150
>> Coords   0
>> Velocities200150
>> Forces   0
>> Box   200150
>>
>> Well, it looks ok. Any suggestions?
>>
>>
>>  On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo  wrote:
>>
>>>  Sorry, I saw now the command line you've posted. Did you check your trr
>>> with gmxcheck?
>>>
>>>
>>> El 09/05/12 15:49, Steven Neumann escribió:
>>>
>>> hello gmx users,
>>>
>>>
>>> I am sorry for bothering you but I was searching mailing list and no
>>> results. I have a problem with my test particle insertion as I run the
>>> workflow I described previously with my mdp:
>>>
>>> title   = Test Particle Insertion
>>> ; Run parameters
>>> integrator  = tpi
>>> nsteps  = 5000; 100 ns
>>> dt  = 0.002 ; 2 fs
>>> ; Output control
>>> nstxout = 0  ; suppress .trr output ; output coordinates
>>> every 25 ps
>>> nstvout = 25000 ; velocities to output every 25000 steps
>>> nstenergy   = 1000  ; save energies every 2 ps
>>> nstlog  = 1000  ; update log file every 2 ps
>>> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
>>> energygrps  = System
>>> continuation= no   ; first dynamics run
>>> constraint_algorithm = lincs; holonomic constraints
>>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>>> constrained
>>> lincs_iter  = 1 ; accuracy of LINCS
>>> lincs_order = 4 ; also related to accuracy
>>> ; Neighborsearching
>>> ns_type = grid  ; search neighboring grid cells
>>> nstlist = 5 ; 10 fs
>>> vdwtype = Switch
>>> rvdw-switch = 1.0
>>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
>>> potential rcoulomb
>>> ; Electrostatics
>>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order   = 4 ; cubic interpolation
>>> fourierspacing  = 0.12  ; grid spacing for FFT
>>> ; Temperature coupling is on
>>> tcoupl  = V-rescale ; modified Berendsen
>>> thermostat
>>> tc_grps = System ; two coupling groups - more
>>> accurate
>>> tau_t   = 0.1 ; time constant, in ps
>>> ref_t   = 318 ; reference temperature, one
>>> for each group, in K
>>> ; Pressure coupling is on
>>> pcoupl  = Parrinello-Rahman ; pressure coupling is on
>>> for NPT
>>> pcoupltype  = isotropic ; uniform scaling of box
>>> vectors
>>> tau_p   = 2.0   ; time constant, in ps
>>> ref_p   = 1.0   ; reference pressure, in bar
>>> compressibility = 4.5e-5; isothermal compressibility
>>> of water, bar^-1
>>> ; Periodic boundary conditions
>>> pbc = xyz   ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes   ; assign velocities from Maxwell distribution
>>> gen_temp= 318   ; temperature for Maxwell distribution
>>> gen_seed= -1; generate a random seed
>>>
>>> Then My log file:
>>>
>>>
>>>  The temperature for test particle insertion is 318.000 K
>>>
>>> Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012
>>>
>>> Will insert 3 atoms with partial charges
>>>
>>> Will insert 5000 times in each frame of md318.trr
>>> Will use the same neighborlist for 5 insertions in a sphere of radius
>>> 0.05
>>>
>>> = -nan nm^3
>>>= -nan kJ/mol
>>> No MEGA Flopsen this time
>>>
>>>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>>
>>>  Computing: Nodes Number G-CyclesSeconds %
>>> 

Re: [gmx-users] Test Particle Insertion of Water

[Javier Cerezo]

The trr file has something wrong. Look at "Coords", it has 0 frames

You may have forgotten to set nstxout to a non-zero value?

Javier

El 09/05/12 16:10, Steven Neumann escribió:

I added one water molecule in my topology to all water molecules:

[ molecules ]
; Compound#mols
Alanine40
SOL   724

Maybe I should add aditional line like:

[ molecules ]
; Compound#mols
Alanine40
SOL   723
SOL  1

What do you think?


On Wed, May 9, 2012 at 3:04 PM, Steven Neumann > wrote:


Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  2569
Last frame   2000 time 10.000


Item#frames Timestep (ps)
Step  200150
Time  200150
Lambda200150
Coords   0
Velocities200150
Forces   0
Box   200150

Well, it looks ok. Any suggestions?


On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo mailto:j...@um.es>> wrote:

Sorry, I saw now the command line you've posted. Did you check
your trr with gmxcheck?


El 09/05/12 15:49, Steven Neumann escribió:

hello gmx users,


I am sorry for bothering you but I was searching mailing list
and no results. I have a problem with my test particle
insertion as I run the workflow I described previously with
my mdp:

title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output
coordinates every 25 ps
nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy
atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.2   ; short-range van der Waals cutoff
(in nm)
ewald_rtol  = 1e-5  ; relative strenght of the
Ewald-shifted potential rcoulomb
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for
long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified
Berendsen thermostat
tc_grps = System ; two coupling groups -
more accurate
tau_t   = 0.1 ; time
constant, in ps
ref_t   = 318 ; reference
temperature, one for each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure
coupling is on for NPT
pcoupltype  = isotropic ; uniform scaling
of box vectors
tau_p   = 2.0   ; time constant,
in ps
ref_p   = 1.0   ; reference
pressure, in bar
compressibility = 4.5e-5; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18
2012

Will insert 3 atoms with partial charges

Will insert 5000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere
of radius 0.05

  = -nan nm^3
 = -

Re: [gmx-users] Test Particle Insertion of Water

[Steven Neumann]

I added one water molecule in my topology to all water molecules:

[ molecules ]
; Compound#mols
Alanine40
SOL   724

Maybe I should add aditional line like:

[ molecules ]
; Compound#mols
Alanine40
SOL   723
SOL  1

What do you think?


On Wed, May 9, 2012 at 3:04 PM, Steven Neumann wrote:

> Checking file md.trr
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time0.000
> # Atoms  2569
> Last frame   2000 time 10.000
>
>
> Item#frames Timestep (ps)
> Step  200150
> Time  200150
> Lambda200150
> Coords   0
> Velocities200150
> Forces   0
> Box   200150
>
> Well, it looks ok. Any suggestions?
>
>
> On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo  wrote:
>
>>  Sorry, I saw now the command line you've posted. Did you check your trr
>> with gmxcheck?
>>
>>
>> El 09/05/12 15:49, Steven Neumann escribió:
>>
>> hello gmx users,
>>
>>
>> I am sorry for bothering you but I was searching mailing list and no
>> results. I have a problem with my test particle insertion as I run the
>> workflow I described previously with my mdp:
>>
>> title   = Test Particle Insertion
>> ; Run parameters
>> integrator  = tpi
>> nsteps  = 5000; 100 ns
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 0  ; suppress .trr output ; output coordinates
>> every 25 ps
>> nstvout = 25000 ; velocities to output every 25000 steps
>> nstenergy   = 1000  ; save energies every 2 ps
>> nstlog  = 1000  ; update log file every 2 ps
>> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
>> energygrps  = System
>> continuation= no   ; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> vdwtype = Switch
>> rvdw-switch = 1.0
>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
>> potential rcoulomb
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.12  ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl  = V-rescale ; modified Berendsen
>> thermostat
>> tc_grps = System ; two coupling groups - more accurate
>> tau_t   = 0.1 ; time constant, in ps
>> ref_t   = 318 ; reference temperature, one
>> for each group, in K
>> ; Pressure coupling is on
>> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
>> NPT
>> pcoupltype  = isotropic ; uniform scaling of box
>> vectors
>> tau_p   = 2.0   ; time constant, in ps
>> ref_p   = 1.0   ; reference pressure, in bar
>> compressibility = 4.5e-5; isothermal compressibility
>> of water, bar^-1
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; assign velocities from Maxwell distribution
>> gen_temp= 318   ; temperature for Maxwell distribution
>> gen_seed= -1; generate a random seed
>>
>> Then My log file:
>>
>>
>>  The temperature for test particle insertion is 318.000 K
>>
>> Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012
>>
>> Will insert 3 atoms with partial charges
>>
>> Will insert 5000 times in each frame of md318.trr
>> Will use the same neighborlist for 5 insertions in a sphere of radius
>> 0.05
>>
>> = -nan nm^3
>>= -nan kJ/mol
>> No MEGA Flopsen this time
>>
>>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>
>>  Computing: Nodes Number G-CyclesSeconds %
>> --
>> -
>>  Rest   4   5.2181.9   100.0
>> ---
>>  Total  4   5.2181.9   100.0
>> ---
>>
>> Parallel run - timing based on wallclock.
>>
>>NODE (s)   Real (s)  (%)
>>T

Re: [gmx-users] Test Particle Insertion of Water

[Steven Neumann]

Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  2569
Last frame   2000 time 10.000


Item#frames Timestep (ps)
Step  200150
Time  200150
Lambda200150
Coords   0
Velocities200150
Forces   0
Box   200150

Well, it looks ok. Any suggestions?

On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo  wrote:

>  Sorry, I saw now the command line you've posted. Did you check your trr
> with gmxcheck?
>
>
> El 09/05/12 15:49, Steven Neumann escribió:
>
> hello gmx users,
>
>
> I am sorry for bothering you but I was searching mailing list and no
> results. I have a problem with my test particle insertion as I run the
> workflow I described previously with my mdp:
>
> title   = Test Particle Insertion
> ; Run parameters
> integrator  = tpi
> nsteps  = 5000; 100 ns
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 0  ; suppress .trr output ; output coordinates every
> 25 ps
> nstvout = 25000 ; velocities to output every 25000 steps
> nstenergy   = 1000  ; save energies every 2 ps
> nstlog  = 1000  ; update log file every 2 ps
> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
> energygrps  = System
> continuation= no   ; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> vdwtype = Switch
> rvdw-switch = 1.0
> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted potential
> rcoulomb
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.12  ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc_grps = System ; two coupling groups - more accurate
> tau_t   = 0.1 ; time constant, in ps
> ref_t   = 318 ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
> NPT
> pcoupltype  = isotropic ; uniform scaling of box
> vectors
> tau_p   = 2.0   ; time constant, in ps
> ref_p   = 1.0   ; reference pressure, in bar
> compressibility = 4.5e-5; isothermal compressibility
> of water, bar^-1
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 318   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> Then My log file:
>
>
>  The temperature for test particle insertion is 318.000 K
>
> Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012
>
> Will insert 3 atoms with partial charges
>
> Will insert 5000 times in each frame of md318.trr
> Will use the same neighborlist for 5 insertions in a sphere of radius
> 0.05
>
> = -nan nm^3
>= -nan kJ/mol
> No MEGA Flopsen this time
>
>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes Number G-CyclesSeconds %
> --
> -
>  Rest   4   5.2181.9   100.0
> ---
>  Total  4   5.2181.9   100.0
> ---
>
> Parallel run - timing based on wallclock.
>
>NODE (s)   Real (s)  (%)
>Time:  0.485  0.485100.0
>(Mnbf/s)   (MFlops)   (steps/hour)
> Performance:  0.000  0.0000.0
> Finished mdrun on node 0 Wed May  9 14:18:19 2012
>
>
>
> Files are empty. Do you have any clue what is happening?
>
> Thank you for your time,
>
> Steven
>
>
> On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo  wrote:
>
>>  Hi Steven
>>
>> As I remember, TPI is based on the calculation of the potential at every
>> conformation from the already computed simulation (inserting

Re: [gmx-users] Test Particle Insertion of Water

[Javier Cerezo]

Sorry, I saw now the command line you've posted. Did you check your trr 
with gmxcheck?


El 09/05/12 15:49, Steven Neumann escribió:

hello gmx users,

I am sorry for bothering you but I was searching mailing list and no 
results. I have a problem with my test particle insertion as I run the 
workflow I described previously with my mdp:


title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output coordinates 
every 25 ps

nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted 
potential rcoulomb

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen 
thermostat

tc_grps = System ; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 318 ; reference temperature, one 
for each group, in K

; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure coupling is on 
for NPT
pcoupltype  = isotropic ; uniform scaling of box 
vectors

tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal 
compressibility of water, bar^-1

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012

Will insert 3 atoms with partial charges

Will insert 5000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere of radius 
0.05


  = -nan nm^3
 = -nan kJ/mol
No MEGA Flopsen this time

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
--
-
 Rest   4   5.2181.9   100.0
---
 Total  4   5.2181.9   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  0.485  0.485100.0
   (Mnbf/s)   (MFlops)   (steps/hour)
Performance:  0.000  0.0000.0
Finished mdrun on node 0 Wed May  9 14:18:19 2012



Files are empty. Do you have any clue what is happening?

Thank you for your time,

Steven


On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo > wrote:


Hi Steven

As I remember, TPI is based on the calculation of the potential at
every conformation from the already computed simulation (inserting
the particle in every snapshot), so velocities are not used.

Anyway, use both and see if there are any differences.

Javier

El 09/05/12 11:27, Steven Neumann escribió:

Dear Gmx Users,

I am running TPI of the water in the system containing free amino
acids. Steps:

1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file
(converted from gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra
water molecule
4. mdrun --s tpi298.tpr -rerun md298.trr -deffnm tpi298 -t

Re: [gmx-users] Test Particle Insertion of Water

[Steven Neumann]

grompp -f tpi.mdp -c tpi.pdb -p topol.top -o tpi.tpr

where tpi.pdb is a file with extra water molecule as well as topol.top.
Then:

mdrun –s tpi.tpr -rerun md.trr -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg



On Wed, May 9, 2012 at 2:56 PM, Javier Cerezo  wrote:

> What's your command line?
>
> El 09/05/12 15:49, Steven Neumann escribió:
>
>  title   = Test Particle Insertion
>> ; Run parameters
>> integrator  = tpi
>> nsteps  = 5000; 100 ns
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 0  ; suppress .trr output ; output coordinates
>> every 25 ps
>> nstvout = 25000 ; velocities to output every 25000 steps
>> nstenergy   = 1000  ; save energies every 2 ps
>> nstlog  = 1000  ; update log file every 2 ps
>> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
>> energygrps  = System
>> continuation= no   ; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> vdwtype = Switch
>> rvdw-switch = 1.0
>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
>> potential rcoulomb
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.12  ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl  = V-rescale ; modified Berendsen
>> thermostat
>> tc_grps = System ; two coupling groups - more accurate
>> tau_t   = 0.1 ; time constant, in ps
>> ref_t   = 318 ; reference temperature, one
>> for each group, in K
>> ; Pressure coupling is on
>> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
>> NPT
>> pcoupltype  = isotropic ; uniform scaling of box
>> vectors
>> tau_p   = 2.0   ; time constant, in ps
>> ref_p   = 1.0   ; reference pressure, in bar
>> compressibility = 4.5e-5; isothermal compressibility
>> of water, bar^-1
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; assign velocities from Maxwell distribution
>> gen_temp= 318   ; temperature for Maxwell distribution
>> gen_seed= -1; generate a random seed
>>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water

[Javier Cerezo]

What's your command line?

El 09/05/12 15:49, Steven Neumann escribió:

title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output coordinates 
every 25 ps

nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted 
potential rcoulomb

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen 
thermostat

tc_grps = System ; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 318 ; reference temperature, one 
for each group, in K

; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure coupling is on 
for NPT
pcoupltype  = isotropic ; uniform scaling of box 
vectors

tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal 
compressibility of water, bar^-1

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water

[Steven Neumann]

hello gmx users,

I am sorry for bothering you but I was searching mailing list and no
results. I have a problem with my test particle insertion as I run the
workflow I described previously with my mdp:

title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output coordinates every
25 ps
nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc_grps = System ; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 318 ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012

Will insert 3 atoms with partial charges

Will insert 5000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere of radius
0.05

= -nan nm^3
   = -nan kJ/mol
No MEGA Flopsen this time

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
--
-
 Rest   4   5.2181.9   100.0
---
 Total  4   5.2181.9   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  0.485  0.485100.0
   (Mnbf/s)   (MFlops)   (steps/hour)
Performance:  0.000  0.0000.0
Finished mdrun on node 0 Wed May  9 14:18:19 2012



Files are empty. Do you have any clue what is happening?

Thank you for your time,

Steven


On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo  wrote:

>  Hi Steven
>
> As I remember, TPI is based on the calculation of the potential at every
> conformation from the already computed simulation (inserting the particle
> in every snapshot), so velocities are not used.
>
> Anyway, use both and see if there are any differences.
>
> Javier
>
> El 09/05/12 11:27, Steven Neumann escribió:
>
> Dear Gmx Users,
>
> I am running TPI of the water in the system containing free amino acids.
> Steps:
>
> 1. I run the NPT simulation of 100 ns to equilibrate the system.
> 2. I added 1 extra water molecule to the final pdb file (converted from
> gro) and to topology
> 3. I creaded tpi.tpr using grompp using new pdb file with extra water
> molecule
> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
> -tpid tpid298.xvg
>
> My question: Is it better generate new velocities in my mdp file
> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
> velocities from pre

Re: [gmx-users] Test Particle Insertion of Water

[Steven Neumann]

thank you Javier, I will try both in this case.

On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo  wrote:

>  Hi Steven
>
> As I remember, TPI is based on the calculation of the potential at every
> conformation from the already computed simulation (inserting the particle
> in every snapshot), so velocities are not used.
>
> Anyway, use both and see if there are any differences.
>
> Javier
>
> El 09/05/12 11:27, Steven Neumann escribió:
>
> Dear Gmx Users,
>
> I am running TPI of the water in the system containing free amino acids.
> Steps:
>
> 1. I run the NPT simulation of 100 ns to equilibrate the system.
> 2. I added 1 extra water molecule to the final pdb file (converted from
> gro) and to topology
> 3. I creaded tpi.tpr using grompp using new pdb file with extra water
> molecule
> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
> -tpid tpid298.xvg
>
> My question: Is it better generate new velocities in my mdp file
> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
> velocities from previous simulations (gro file)?
> If the second option is more appropriate what velocity shall I adjust to
> the extra water molecule?
>
> I will appreciate your reply.
>
> Steven
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water

[Javier Cerezo]

Hi Steven

As I remember, TPI is based on the calculation of the potential at every 
conformation from the already computed simulation (inserting the 
particle in every snapshot), so velocities are not used.


Anyway, use both and see if there are any differences.

Javier

El 09/05/12 11:27, Steven Neumann escribió:

Dear Gmx Users,

I am running TPI of the water in the system containing free amino 
acids. Steps:


1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file (converted 
from gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra water 
molecule
4. mdrun --s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi 
tpi298.xvg -tpid tpid298.xvg


My question: Is it better generate new velocities in my mdp file 
(continuation = yes, gen_vel = no, tpi integrator) for a pdb file or 
use velocities from previous simulations (gro file)?
If the second option is more appropriate what velocity shall I adjust 
to the extra water molecule?


I will appreciate your reply.

Steven




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Physical Chemistry
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[gmx-users] Test Particle Insertion of Water

[Steven Neumann]

Dear Gmx Users,

I am running TPI of the water in the system containing free amino acids.
Steps:

1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file (converted from
gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra water
molecule
4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
-tpid tpid298.xvg

My question: Is it better generate new velocities in my mdp file
(continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
velocities from previous simulations (gro file)?
If the second option is more appropriate what velocity shall I adjust to
the extra water molecule?

I will appreciate your reply.

Steven
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[gmx-users] Test particle insertion extra coordinate

[MPID]

Hi everyone. I am trying to do test particle insertion in a cavity with the
tpic option. The manual says that the trajectory file should have one extra
coordinate for the cavity location. I have a trajectory from an md run that
I would like to use. How do I get the extra coordinate in there, and where
does it belong in order? Sorry if this is a dumb question, but I searched
the archives and still couldn't figure out an answer.

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RE: [gmx-users] Test mail

[victor doss]

ok

Date: Sat, 17 Dec 2011 16:33:25 +0530
From: priya.thiyagaraja...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Test mail

Greetings, THis is a mail to test my gromacs mailing list connection


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[gmx-users] Test mail

[priya thiyagarajan]

Greetings, THis is a mail to test my gromacs mailing list connection
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[gmx-users] test on g_density

[chris . neale]

Could it be this:

http://www.mail-archive.com/gmx-users@gromacs.org/msg35107.html

I've posted a few times on the fact that this tool is broken for  
constant pressure simulations.


I'm not sure why both even and odd would be under the overall average,  
but it seems possible.


Chris.

-- original message --


Hi all.

I've noticed an unexpected behaviour using g_density. I have a
trajectory (with time step 2) and it is split into two subsets (using
trjconv) with, lets say, even and odd steps respectively. According
the the algorithm I expected that the density obtained with the
original trajectory would be the average of the density with each
generated trajectory. However, that was not the case, and for each
slice, while density calculated from the subsets was practically the
same, the density calculated with the original was different (greater
or lower). My system is a membrane, the original trajectory is 50ns
long (25001 steps) and I calculate the density along the bilayer
normal (z). I am using GROMACS4.5.3 and a I've issued the following
commands:

*To get the subsets:
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_odd -dt 4
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_even -dt 4 -b 2

The generated trajectories have 12501 and 12500 steps respectively.

*To calculate the densities:
g_density -f bilayer.xtc -s bilayer.tpr -o dens_all
g_density -f bilayer_odd.xtc -s bilayer.tpr -o dens_odd
g_density -f bilayer_even.xtc -s bilayer.tpr -o dens_even

The result is attached. dens_odd and dens_even are very similar, but
surprisingly (at least for me), dens_all is different (it actually
integrates more atoms than the other two).

I haven't seen anything in the code that could explain that result
(maybe when removing pbc??). Is it a bug or a mistake from me?

Thank you!

Javier
-- next part --


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[gmx-users] test on g_density

[JAVIER CEREZO BASTIDA]

Hi all.

I've noticed an unexpected behaviour using g_density. I have a  
trajectory (with time step 2) and it is split into two subsets (using  
trjconv) with, lets say, even and odd steps respectively. According  
the the algorithm I expected that the density obtained with the  
original trajectory would be the average of the density with each  
generated trajectory. However, that was not the case, and for each  
slice, while density calculated from the subsets was practically the  
same, the density calculated with the original was different (greater  
or lower). My system is a membrane, the original trajectory is 50ns  
long (25001 steps) and I calculate the density along the bilayer  
normal (z). I am using GROMACS4.5.3 and a I've issued the following  
commands:


*To get the subsets:
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_odd -dt 4
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_even -dt 4 -b 2

The generated trajectories have 12501 and 12500 steps respectively.

*To calculate the densities:
g_density -f bilayer.xtc -s bilayer.tpr -o dens_all
g_density -f bilayer_odd.xtc -s bilayer.tpr -o dens_odd
g_density -f bilayer_even.xtc -s bilayer.tpr -o dens_even

The result is attached. dens_odd and dens_even are very similar, but  
surprisingly (at least for me), dens_all is different (it actually  
integrates more atoms than the other two).


I haven't seen anything in the code that could explain that result  
(maybe when removing pbc??). Is it a bug or a mistake from me?


Thank you!

Javier


g_density_test.pdf
Description: Adobe PDF document
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[gmx-users] Test

[Justin A. Lemkul]

My messages haven't been going through since yesterday, testing to see if this 
one makes it.


--


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


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[gmx-users] Test

[Rossen Apostolov]

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[gmx-users] Test

[David van der Spoel]

Hi,

this is a test to see whether the mailing list works.

Cheers,
--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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RE: [gmx-users] test particle insertion with PME

[Berk Hess]

Hi,

Yes, I implemented it in git master.

Berk

> From: schn...@uni-heidelberg.de
> Date: Mon, 15 Mar 2010 14:52:38 +0100
> To: gmx-users@gromacs.org
> Subject: [gmx-users] test particle insertion with PME
> 
> Hi all,
> 
> has the combination of tpi (test particle insertion) and PME (particle  
> mesh Ewald) already been implemented into any GROMACS version?
> 
> Eamnuel
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[gmx-users] test particle insertion with PME

[Schneck]

Hi all,

has the combination of tpi (test particle insertion) and PME (particle  
mesh Ewald) already been implemented into any GROMACS version?


Eamnuel
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Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Mark Abraham]

YH wrote:
> Dear Dr.  Saavedra,
> 
> I would like to ask your help for my use of Gromacs.
> Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems 
> like the following.
> Would you please tell me how to sovle it. 
> 
> Thank you very much in advanc,
> 
> James, Wang(Dr.)
> Dalian university of Technology, 
> China
> -
>  
>   Back Off! I just backed up pr1.log to ./#pr1.log.5#
> Reading file pr1.tpr, VERSION 4.0.5 (single precision)
> Will use 10 particle-particle and 6 PME only nodes
> This is a guess, check the performance at the end of the log file
> ---
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: domdec.c, line: 5873
> Fatal error:
> There is no domain decomposition for 10 nodes that is compatible with the 
> given box and a minimum cell size of 0.96025 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS 
> settings
> Look in the log file for details on the domain decomposition
> ---

You should read about the domain decomposition algorithm in the manual.
Probably your system is too small to make effective use of this many
processors with this algorithm.

Mark
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[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[YH]

Dear Dr.  Saavedra,

I would like to ask your help for my use of Gromacs.
Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems 
like the following.
Would you please tell me how to sovle it. 

Thank you very much in advanc,

James, Wang(Dr.)
Dalian university of Technology, 
China
-
 
Back Off! I just backed up pr1.log to ./#pr1.log.5#
Reading file pr1.tpr, VERSION 4.0.5 (single precision)
Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
---
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 5873
Fatal error:
There is no domain decomposition for 10 nodes that is compatible with the given 
box and a minimum cell size of 0.96025 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
Look in the log file for details on the domain decomposition
---
"Baseball Heroes Only" (P.J. Harvey)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 16
rank 15 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 15: return code 0 
rank 14 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 14: return code 0 
rank 12 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 12: return code 0 
rank 11 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 11: return code 0 
rank 9 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 9: return code 0 
rank 8 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 8: return code 0 
rank 7 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 7: return code 0 
rank 6 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 6: return code 0 
rank 4 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 4: return code 0 
rank 2 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 2: return code 0 
rank 1 in job 1  node1_50926   caused collective abort of all ranks
  exit status of rank 1: return code 0 
[ma...@node1 seed]$ 

致
礼！


YH
dcp...@sina.com
　　2009-08-22
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Re: [gmx-users] Test suit failures

[Mark Abraham]

Bert wrote:

Dear gmx-users,

I have done a test using test suit 4.0.4, and I got some failures as follows.

All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water


Those fail frequently on normal installations because they are 
susceptible to differences in the virial.



4 out of 14 complex tests FAILED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED


These are caused by a known bug in GROMACS.


All 45 pdb2gmx tests PASSED

My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the
same failures on my Xeon 8 core based linux. For example, in
/kernel/kernel020


You'll probably be fine if you either upgrade your gcc version or learn 
that your particular 4.1.x series compiler has its bugs fixed.


Mark
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Re: [gmx-users] Test suit failures

[Justin A. Lemkul]

Bert wrote:

Dear gmx-users,

I have done a test using test suit 4.0.4, and I got some failures as follows.

All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED


Check the files in these directories to see if the differences are acceptable, 
as explained on the wiki:


http://wiki.gromacs.org/index.php/Test-Set




16 out of 63 kernel tests FAILED


These failures are a known issue and a bugzilla has been filed.  They affect 
Buckingham interactions.



All 45 pdb2gmx tests PASSED

My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the
same failures on my Xeon 8 core based linux. For example, in
/kernel/kernel020



As warned on the Gromacs site: "WARNING: do not use the gcc 4.1.x set of 
compilers. They are broken. These compilers come with recent Linux distrubutions 
like Fedora 5/6 etc."


Users have reported non-functional or improperly-functioning executables 
produced by the 4.1.x series.


-Justin


checkpot.out gives:
--
comparing energy file reference_s.edr and ener.edr

There are 39 terms in the energy files

There are 12 terms to compare in the energy files

LJ-14step   0:  -63.1209,  step   0:  6.50742
Potentialstep   0:  -321.601,  step   0: -251.972

Files read succesfully
--
checkvir.out gives:
--
comparing energy file reference_s.edr and ener.edr

There are 39 terms in the energy files

There are 25 terms to compare in the energy files

LJ-14step   0:  -63.1209,  step   0:  6.50742
Potentialstep   0:  -321.601,  step   0: -251.972
Kinetic En.  step   0:   15.0135,  step   0:  29.0739
Total Energy step   0:  -306.588,  step   0: -222.898
Temperature  step   0:   1.93226,  step   0:  3.74185
Pressure (bar)   step   0:  -3095.37,  step   0: -2497.79
Vir-XX   step   0:   1127.45,  step   0:  1075.85
Vir-XY   step   0:63.524,  step   0:  21.7761
Vir-XZ   step   0:  -264.813,  step   0: -260.354
Vir-YX   step   0:   63.5241,  step   0:   21.777
Vir-YY   step   0:   803.252,  step   0:  581.702
Vir-ZX   step   0:  -264.813,  step   0: -260.354
Vir-ZZ   step   0:   321.207,  step   0:  176.573

Files read succesfully

The deviations are obvious. Any suggestion would be appreciate. Thank you.

Best Regards,
Bert
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--


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


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[gmx-users] Test suit failures

[Bert]

Dear gmx-users,

I have done a test using test suit 4.0.4, and I got some failures as follows.

All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED

My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the
same failures on my Xeon 8 core based linux. For example, in
/kernel/kernel020

checkpot.out gives:
--
comparing energy file reference_s.edr and ener.edr

There are 39 terms in the energy files

There are 12 terms to compare in the energy files

LJ-14step   0:  -63.1209,  step   0:  6.50742
Potentialstep   0:  -321.601,  step   0: -251.972

Files read succesfully
--
checkvir.out gives:
--
comparing energy file reference_s.edr and ener.edr

There are 39 terms in the energy files

There are 25 terms to compare in the energy files

LJ-14step   0:  -63.1209,  step   0:  6.50742
Potentialstep   0:  -321.601,  step   0: -251.972
Kinetic En.  step   0:   15.0135,  step   0:  29.0739
Total Energy step   0:  -306.588,  step   0: -222.898
Temperature  step   0:   1.93226,  step   0:  3.74185
Pressure (bar)   step   0:  -3095.37,  step   0: -2497.79
Vir-XX   step   0:   1127.45,  step   0:  1075.85
Vir-XY   step   0:63.524,  step   0:  21.7761
Vir-XZ   step   0:  -264.813,  step   0: -260.354
Vir-YX   step   0:   63.5241,  step   0:   21.777
Vir-YY   step   0:   803.252,  step   0:  581.702
Vir-ZX   step   0:  -264.813,  step   0: -260.354
Vir-ZZ   step   0:   321.207,  step   0:  176.573

Files read succesfully

The deviations are obvious. Any suggestion would be appreciate. Thank you.

Best Regards,
Bert
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RE: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Harry Saavedra]

Hi,
My system is composed of 900 copies of the same small molecule without charges 
(atoms a1, a2, a3 + a virtual site). All the atoms a1..a3 interact using a 
tabulated potential 1 and all the virtual sites of every molecule interact 
using tabulated potential 2. (The system has two energy groups). This is the 
reason why I wanted to use two energy groups in the test particle.

For curiosity, does Gromacs use the Cavity Insertion Widom method?

Thanks for the advice !

Harry G.

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
Date: Fri, 15 May 2009 09:18:56 +0200








Hi,

The issue is slightly different here.
Currently TPI in Gromacs is limited to inserting a single charge group.
Since energy groups should consist of whole charge groups, the inserted
molecule can only consist of a single energy group.
You can solve your problem by making the whole inserted molecule an energy 
group C
and then define the proper tables between A-C and B-C.

I have no clue how your system looks like, but if you have multiple charge 
groups,
won't you molecule be to large for use with TPI?
TPI will only work for molecules that are small enough to fit into spontaneously
occurring cavities.

Berk

> Date: Fri, 15 May 2009 07:50:52 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
> 
> Harry Saavedra wrote:
> > Dear All,
> > 
> > I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
> > molecules of the system work with two energy groups (two tabulated 
> > potentials), and every atom belongs to a different charge group; but 
> > Gromacs shows an error message:
> > 
> >  > grompp...
> >  > mdrun ...
> > 
> > Program mdrun, VERSION 4.0.3
> > Source code file: force.c, line: 1068 Send 
> > Fatal error:
> > The molecule to insert can not consist of multiple charge groups.
> > Make it a single charge group.
> > 
> > 
> > However,when I set all the atoms of the inserted molecule (A,B,C..) to 
> > the same charge group (cgnr in the top file), Gromacs displays :
> > 
> > 
> >  >grompp...
> > 
> > Program grompp, VERSION 4.0.3
> > Source code file: grompp.c, line: 150
> > Fatal error:
> > atoms A and B in charge group Z of molecule type 'Protein' are in 
> > different energy groups
> > 
> > 
> > There is any way to overcome this problem? How Gromacs can ignore the 
> > charge groups?
> 
> Energy groups are set in the .mdp file using the groups defined 
> (implicitly) in the .ndx file. You need a charge group that is a subset 
> of a single energy group.
> 
> Mark
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RE: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Berk Hess]

Hi,

The issue is slightly different here.
Currently TPI in Gromacs is limited to inserting a single charge group.
Since energy groups should consist of whole charge groups, the inserted
molecule can only consist of a single energy group.
You can solve your problem by making the whole inserted molecule an energy 
group C
and then define the proper tables between A-C and B-C.

I have no clue how your system looks like, but if you have multiple charge 
groups,
won't you molecule be to large for use with TPI?
TPI will only work for molecules that are small enough to fit into spontaneously
occurring cavities.

Berk

> Date: Fri, 15 May 2009 07:50:52 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
> 
> Harry Saavedra wrote:
> > Dear All,
> > 
> > I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
> > molecules of the system work with two energy groups (two tabulated 
> > potentials), and every atom belongs to a different charge group; but 
> > Gromacs shows an error message:
> > 
> >  > grompp...
> >  > mdrun ...
> > 
> > Program mdrun, VERSION 4.0.3
> > Source code file: force.c, line: 1068 Send 
> > Fatal error:
> > The molecule to insert can not consist of multiple charge groups.
> > Make it a single charge group.
> > 
> > 
> > However,when I set all the atoms of the inserted molecule (A,B,C..) to 
> > the same charge group (cgnr in the top file), Gromacs displays :
> > 
> > 
> >  >grompp...
> > 
> > Program grompp, VERSION 4.0.3
> > Source code file: grompp.c, line: 150
> > Fatal error:
> > atoms A and B in charge group Z of molecule type 'Protein' are in 
> > different energy groups
> > 
> > 
> > There is any way to overcome this problem? How Gromacs can ignore the 
> > charge groups?
> 
> Energy groups are set in the .mdp file using the groups defined 
> (implicitly) in the .ndx file. You need a charge group that is a subset 
> of a single energy group.
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Mark Abraham]

Harry Saavedra wrote:

Dear All,

I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
molecules of the system work with two energy groups (two tabulated 
potentials), and every atom belongs to a different charge group; but 
Gromacs shows an error message:


 > grompp...
 > mdrun ...

Program mdrun, VERSION 4.0.3
Source code file: force.c, line: 1068 Send 
Fatal error:
The molecule to insert can not consist of multiple charge groups.
Make it a single charge group.


However,when I set all the atoms of the inserted molecule (A,B,C..) to 
the same charge group (cgnr in the top file), Gromacs displays :



 >grompp...

Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 150
Fatal error:
atoms A and B in charge group Z of molecule type 'Protein' are in 
different energy groups



There is any way to overcome this problem? How Gromacs can ignore the 
charge groups?


Energy groups are set in the .mdp file using the groups defined 
(implicitly) in the .ndx file. You need a charge group that is a subset 
of a single energy group.


Mark
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[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Harry Saavedra]

Dear All,

I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
molecules of the system work with two energy groups (two tabulated potentials), 
and every atom belongs to a different charge group; but Gromacs shows an error 
message: 

> grompp...
> mdrun ...

Program mdrun, VERSION 4.0.3
Source code file: force.c, line: 1068
Send
Fatal error:
The molecule to insert can not consist of multiple charge groups.
Make it a single charge group.


However,when I set all the atoms of the inserted molecule (A,B,C..) to the same 
charge group (cgnr in the top file), Gromacs displays :


>grompp... 

Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 150
Fatal error:
atoms A and B in charge group Z of molecule type 'Protein' are in different 
energy groups


There is any way to overcome this problem? How Gromacs can ignore the charge 
groups? 



Thanks in advance,


Harry Gustavo

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[gmx-users] Test-set

[Zhanglin Ni]

Thanks, Justin. Then does it mean I cannot use the program to do simulation 
at this point? any suggestion on it?

Johnny


Date: Fri, 08 May 2009 12:31:31 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a045e63.1080...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Zhanglin Ni wrote:

The configurations are
Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2
20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009
CPU1: Intel(R) Core(TM)2 Duo CPU E7400  @ 2.80GHz stepping 0a
lspci
00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM
Controller (rev 10)
00:02.0 VGA compatible controller: Intel Corporation 82G33/G31 Express
Integrated Graphics Controller (rev 10)
00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High
Definition Audio Controller (rev 01)
00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #1 (rev 01)
00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #2 (rev 01)
00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #3 (rev 01)
00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #4 (rev 01)
00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI
Controller (rev 01)
00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev e1)
00:1f.0 ISA bridge: Intel Corporation 82801GB/GR (ICH7 Family) LPC
Interface Bridge (rev 01)
00:1f.2 IDE interface: Intel Corporation 82801GB/GR/GH (ICH7 Family)
SATA IDE Controller (rev 01)
00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller
(rev 01)
01:08.0 Ethernet controller: Intel Corporation 82801G (ICH7 Family) LAN
Controller (rev 01)

FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water

The water test seems was the worse one. it showed like


Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999




When I run the test set on my system (dual-core Intel MacBook), I get this 
in

the tail end of the checkvir.out for water:

Pressure (bar)   step  50:   46893.3,  step  50:  45119.8
Vir-XX   step  50:  -6211.69,  step  50: -6436.94
Vir-XY   step  50:  -2423.21,  step  50: -1896.98
Vir-XZ   step  50:   667.327,  step  50:  316.873
Vir-YX   step  50:  -2422.22,  step  50: -1896.65
Vir-YY   step  50:  -3194.86,  step  50: -2648.67
Vir-YZ   step  50:   -2208.7,  step  50: -2641.28
Vir-ZX   step  50:   667.878,  step  50:  318.282
Vir-ZY   step  50:  -2207.77,  step  50: -2640.33
Vir-ZZ   step  50:  -1482.41,  step  50: -817.011

It seems that your system is not producing the Vir-XX component, which may 
be

what's causing the failure.  The magnitude of difference between the other
energy terms is not substantially different from what I see (and my test 
passes).


I now also recall you reported the following originally in your 
checkpot.out:


There are 30 terms in the energy files

In my checkpot.out, the line reads:

There are 31 terms in the energy files

I suspect that is where the problem lies, but that is also where my 
usefulness
ends.  Perhaps one of the developers can comment at this point as to the 
reason

for the missing energy term.

-Justin


Thanks
Johnny


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Re: [gmx-users] Test-set

[Justin A. Lemkul]

Zhanglin Ni wrote:

The configurations are
Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2 
20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009

CPU1: Intel(R) Core(TM)2 Duo CPU E7400  @ 2.80GHz stepping 0a
lspci
00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM 
Controller (rev 10)
00:02.0 VGA compatible controller: Intel Corporation 82G33/G31 Express 
Integrated Graphics Controller (rev 10)
00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High 
Definition Audio Controller (rev 01)
00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #1 (rev 01)
00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #2 (rev 01)
00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #3 (rev 01)
00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #4 (rev 01)
00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI 
Controller (rev 01)

00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev e1)
00:1f.0 ISA bridge: Intel Corporation 82801GB/GR (ICH7 Family) LPC 
Interface Bridge (rev 01)
00:1f.2 IDE interface: Intel Corporation 82801GB/GR/GH (ICH7 Family) 
SATA IDE Controller (rev 01)
00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller 
(rev 01)
01:08.0 Ethernet controller: Intel Corporation 82801G (ICH7 Family) LAN 
Controller (rev 01)


FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water

The water test seems was the worse one. it showed like


Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999




When I run the test set on my system (dual-core Intel MacBook), I get this in 
the tail end of the checkvir.out for water:


Pressure (bar)   step  50:   46893.3,  step  50:  45119.8
Vir-XX   step  50:  -6211.69,  step  50: -6436.94
Vir-XY   step  50:  -2423.21,  step  50: -1896.98
Vir-XZ   step  50:   667.327,  step  50:  316.873
Vir-YX   step  50:  -2422.22,  step  50: -1896.65
Vir-YY   step  50:  -3194.86,  step  50: -2648.67
Vir-YZ   step  50:   -2208.7,  step  50: -2641.28
Vir-ZX   step  50:   667.878,  step  50:  318.282
Vir-ZY   step  50:  -2207.77,  step  50: -2640.33
Vir-ZZ   step  50:  -1482.41,  step  50: -817.011

It seems that your system is not producing the Vir-XX component, which may be 
what's causing the failure.  The magnitude of difference between the other 
energy terms is not substantially different from what I see (and my test passes).


I now also recall you reported the following originally in your checkpot.out:

There are 30 terms in the energy files

In my checkpot.out, the line reads:

There are 31 terms in the energy files

I suspect that is where the problem lies, but that is also where my usefulness 
ends.  Perhaps one of the developers can comment at this point as to the reason 
for the missing energy term.


-Justin


Thanks
Johnny



Message: 1
Date: Thu, 07 May 2009 21:50:45 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a038ff5.3030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Zhanglin Ni wrote:

The checkvir.out files looked like (I just show last few lines here):
Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999
Files read succesfully



Which failed test does this correspond to?

At this point, it would also be appropriate to report your system 
configuration
- your OS, version, which compilers were used (and version), hardware, 
and

anything else necessary to diagnose the problem.

-Justin



-Johnny

[gmx-users] Test-set

[Zhanglin Ni]

The configurations are
Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2 20081105 
(Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009

CPU1: Intel(R) Core(TM)2 Duo CPU E7400  @ 2.80GHz stepping 0a
lspci
00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM 
Controller (rev 10)
00:02.0 VGA compatible controller: Intel Corporation 82G33/G31 Express 
Integrated Graphics Controller (rev 10)
00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High Definition 
Audio Controller (rev 01)
00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #1 (rev 01)
00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #2 (rev 01)
00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #3 (rev 01)
00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI 
Controller #4 (rev 01)
00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI 
Controller (rev 01)

00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev e1)
00:1f.0 ISA bridge: Intel Corporation 82801GB/GR (ICH7 Family) LPC Interface 
Bridge (rev 01)
00:1f.2 IDE interface: Intel Corporation 82801GB/GR/GH (ICH7 Family) SATA 
IDE Controller (rev 01)
00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller (rev 
01)
01:08.0 Ethernet controller: Intel Corporation 82801G (ICH7 Family) LAN 
Controller (rev 01)


FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water

The water test seems was the worse one. it showed like


Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999


Thanks
Johnny



Message: 1
Date: Thu, 07 May 2009 21:50:45 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a038ff5.3030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Zhanglin Ni wrote:

The checkvir.out files looked like (I just show last few lines here):
Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999
Files read succesfully



Which failed test does this correspond to?

At this point, it would also be appropriate to report your system 
configuration

- your OS, version, which compilers were used (and version), hardware, and
anything else necessary to diagnose the problem.

-Justin



-Johnny



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RE: [gmx-users] Test-set

[Dallas B. Warren]

Sorry, but I only performed a couple of runs using the test-set, so
don't have a lot of experience, but when I did and got some fails all
the information was there to help point out what the issue was.

Doesn't the files in the subdirectories for each of the tests provide
details of why that particular test failed?

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail
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Re: [gmx-users] Test-set

[Justin A. Lemkul]

Zhanglin Ni wrote:

The checkvir.out files looked like (I just show last few lines here):
Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999
Files read succesfully



Which failed test does this correspond to?

At this point, it would also be appropriate to report your system configuration 
- your OS, version, which compilers were used (and version), hardware, and 
anything else necessary to diagnose the problem.


-Justin



-Johnny



Message: 1
Date: Thu, 07 May 2009 12:44:23 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a030fe7.2030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Any clues from any of the other *.out files?

-Justin

Zhanglin Ni wrote:

Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny




Zhanglin Ni wrote:

Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. 
the

installation seemed no problem at all.  afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED


So check the output of these tests; small rounding errors are
insignificant and
can cause the test to fail (as described on the wiki).

The kernel failures you cite below have been reported before:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

-Justin


FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED

How I can do to solve the problem since it was just installed. Thanks
Johnny




Message: 1
Date: Thu, 07 May 2009 12:44:23 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a030fe7.2030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Any clues from any of the other *.out files?

-Justin

Zhanglin Ni wrote:

Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny




Zhanglin Ni wrote:

Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. 
the

installation seemed no problem at all.  afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED


So check the output of these tests; small rounding errors are
insignificant and
can cause the test to fail (as described on the wiki).

The kernel failures you cite below have been reported before:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

-Justin


FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED

How I can do to solve the problem since it was just installed. Thanks
Johnny



___

[gmx-users] Test-set

[Zhanglin Ni]

The checkvir.out files looked like (I just show last few lines here):
Pressure (bar)   step  50:   46893.3,  step  50:44603
Vir-XY   step  50:  -2423.21,  step  50:  -1880.2
Vir-XZ   step  50:   667.327,  step  50:  307.438
Vir-YX   step  50:  -2422.22,  step  50: -1880.23
Vir-YY   step  50:  -3194.86,  step  50: -2655.73
Vir-YZ   step  50:   -2208.7,  step  50:  -2608.7
Vir-ZX   step  50:   667.878,  step  50:  308.434
Vir-ZY   step  50:  -2207.77,  step  50: -2608.41
Vir-ZZ   step  50:  -1482.41,  step  50: -680.999
Files read succesfully


-Johnny



Message: 1
Date: Thu, 07 May 2009 12:44:23 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a030fe7.2030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Any clues from any of the other *.out files?

-Justin

Zhanglin Ni wrote:

Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny




Zhanglin Ni wrote:

Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all.  afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED


So check the output of these tests; small rounding errors are
insignificant and
can cause the test to fail (as described on the wiki).

The kernel failures you cite below have been reported before:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

-Justin


FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED

How I can do to solve the problem since it was just installed. Thanks
Johnny




Message: 1
Date: Thu, 07 May 2009 12:44:23 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users 
Message-ID: <4a030fe7.2030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Any clues from any of the other *.out files?

-Justin

Zhanglin Ni wrote:

Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny




Zhanglin Ni wrote:

Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all.  afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED


So check the output of these tests; small rounding errors are
insignificant and
can cause the test to fail (as described on the wiki).

The kernel failures you cite below have been reported before:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

-Justin


FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED

How I can do to solve the problem since it was just installed. Thanks
Johnny



___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.or

Re: [gmx-users] Test-set

[Justin A. Lemkul]

Any clues from any of the other *.out files?

-Justin

Zhanglin Ni wrote:

Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny




Zhanglin Ni wrote:

Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all.  afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED


So check the output of these tests; small rounding errors are 
insignificant and

can cause the test to fail (as described on the wiki).

The kernel failures you cite below have been reported before:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

-Justin


FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED

How I can do to solve the problem since it was just installed. Thanks
Johnny


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before 
posting!

Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--


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




--

Message: 6
Date: Thu, 07 May 2009 06:59:21 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] atom name O3PB not found in residue ATP 340
while generating exclusions when running pdb2gmx
To: Discussion list for GROMACS users 
Message-ID: <4a02bf09.4050...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Una Bjarnadottir wrote:

Dear all,

I'm running a simulation of a structure which has part of ATP bound to
it so I'm using the -missing command when running pdb2gmx

pdb2gmx runs and lists the missing atoms and than it gives a fatal error
about missing atom name!

WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
WARNING: atom APG is missing in residue ATP 340 in the pdb file
WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
You might need to add atom H3PG to the hydrogen database of
residue ATP
in the file ff???.hdb (see the manual)

There were 17 missing atoms in molecule Protein_A
Number of bonds was 3730, now 3725
Generating angles, dihedrals and pairs...
Fatal error: atom name O3PB not found in residue ATP 340 while
generating exclusions



The [ exclusions ] are pre-defined in the force field .rtp file.  The 
easiest
way I can see to get around this is to make a local copy of the .rtp 
file, make
a new entry for your molecule based on the ATP entry (deleting out 
whatever
atoms are not present) and trying again, using a new name for this 
partial ATP,

in both the .rtp and .pdb files.

The -missing option, as described by pdb2gmx is "dangerous" for this 
reason.


-Justin

How can I resolve this  first not done by -missing command?

Cheers, Una



--


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




--

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gmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before 
posting!


End of gmx-users Digest, Vol 61, Issue 21
*



___
gmx-users mailing listgmx-

[gmx-users] Test-set

[Zhanglin Ni]

Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny




Zhanglin Ni wrote:

Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all.  afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED


So check the output of these tests; small rounding errors are 
insignificant and

can cause the test to fail (as described on the wiki).

The kernel failures you cite below have been reported before:

http://bugzilla.gromacs.org/show_bug.cgi?id=313

-Justin


FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED

How I can do to solve the problem since it was just installed. Thanks
Johnny


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before 
posting!

Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--


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




--

Message: 6
Date: Thu, 07 May 2009 06:59:21 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] atom name O3PB not found in residue ATP 340
while generating exclusions when running pdb2gmx
To: Discussion list for GROMACS users 
Message-ID: <4a02bf09.4050...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Una Bjarnadottir wrote:

Dear all,

I'm running a simulation of a structure which has part of ATP bound to
it so I'm using the -missing command when running pdb2gmx

pdb2gmx runs and lists the missing atoms and than it gives a fatal error
about missing atom name!

WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
WARNING: atom APG is missing in residue ATP 340 in the pdb file
WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
You might need to add atom H3PG to the hydrogen database of
residue ATP
in the file ff???.hdb (see the manual)

There were 17 missing atoms in molecule Protein_A
Number of bonds was 3730, now 3725
Generating angles, dihedrals and pairs...
Fatal error: atom name O3PB not found in residue ATP 340 while
generating exclusions



The [ exclusions ] are pre-defined in the force field .rtp file.  The 
easiest
way I can see to get around this is to make a local copy of the .rtp file, 
make
a new entry for your molecule based on the ATP entry (deleting out 
whatever
atoms are not present) and trying again, using a new name for this partial 
ATP,

in both the .rtp and .pdb files.

The -missing option, as described by pdb2gmx is "dangerous" for this 
reason.


-Justin

How can I resolve this  first not done by -missing command?

Cheers, Una



--


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




--

___
gmx-users mailing list
gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!

End of gmx-users Digest, Vol 61, Issue 21
*



___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please sea

RE: [gmx-users] test molecule insertion

[Berk Hess]

Hi,

The molecule you want to insert should be a single charge group.
I guess you have miore than one charge group in the molecule.

I will add a check in the code for this, so you get a more
comprehensible error message.

Berk

> Date: Wed, 3 Dec 2008 12:34:23 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] test molecule insertion
> 
> Hi
> I have trouble inserting molecules for test particle insertion (with 
> atoms there is no problem at all).
> I have defined my conf.gro, topology and index files, but it keeps 
> saying that
> "Number of atoms in trajectory (7000) is not equal the number in the run 
> input file (7005) minus the number of atoms to insert (1)"
> How can I define the number of atoms to insert?
> 
> greets
> 
> s.
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_
Express yourself instantly with MSN Messenger! Download today it's FREE!
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[gmx-users] test molecule insertion

[Simon Poblete]

Hi
I have trouble inserting molecules for test particle insertion (with 
atoms there is no problem at all).
I have defined my conf.gro, topology and index files, but it keeps 
saying that
"Number of atoms in trajectory (7000) is not equal the number in the run 
input file (7005) minus the number of atoms to insert (1)"

How can I define the number of atoms to insert?

greets

s.

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Re: [gmx-users] test particle insertion

[Mark Abraham]

Andrei Neamtu wrote:

Hello,

Where can be found more information on test particle insertion method
as implemented in gromacs? It is possible to use molecules as test
particles?


Have you search the manual? It answers your second question.

Mark
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[gmx-users] test particle insertion

[Andrei Neamtu]

Hello,

Where can be found more information on test particle insertion method
as implemented in gromacs? It is possible to use molecules as test
particles?

Thank you a lot,
Andrei
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[gmx-users] Test Set for Gromacs 4?

[Mike Hanby]

Is there a test set available for Gromacs 4?

I looked here and found 3.3.2 and 3.3.3:
ftp://ftp.gromacs.org/pub/tests/

Thanks, Mike
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Re: [gmx-users] Test-set problem with Gromacs 3.3.3

[David van der Spoel]

[EMAIL PROTECTED] wrote:

Dear gmx-users,

I just updated my operating system to Centos 5.1 and Gromacs to version 
3.3.3 and faced some problems with test-set (gmxtest-3.3.2.tgz). I can 
pass all the double precision tests (./gmxtest.pl -double all), but 
number of single precision tests are failed (./gmxtest.pl all). I looked 
at the files for these tests, and noticed that the corresponding tests 
include Coulombic and LJ 1-4 interactions, for which the calculated 
energies are all zero, whereas the reference energies are non-zero with 
values even 1000-2000 kJ/mol. Does anyone know reason for such differences?


This actually points to possible compilation problems, and hence shows 
the value of the test set. Please check every step in the compilation 
process, and also which executable you are running (which mdrun) and 
which libraries (ldd `which mdrun`).





Thanks for your help,

Janne

-- 


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 
Joensuu, FI

Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
-- 


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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Test-set problem with Gromacs 3.3.3

[janne . hirvi]

Dear gmx-users,

I just updated my operating system to Centos 5.1 and Gromacs to  
version 3.3.3 and faced some problems with test-set  
(gmxtest-3.3.2.tgz). I can pass all the double precision tests  
(./gmxtest.pl -double all), but number of single precision tests are  
failed (./gmxtest.pl all). I looked at the files for these tests, and  
noticed that the corresponding tests include Coulombic and LJ 1-4  
interactions, for which the calculated energies are all zero, whereas  
the reference energies are non-zero with values even 1000-2000 kJ/mol.  
Does anyone know reason for such differences?


Thanks for your help,

Janne

--
Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
--
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