[gmx-users] Test Particle Insertion
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! * 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
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. anhp...@ou.edu 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! * 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 -- Naga Rajesh Tummala, PhD Post-Doctoral Researcher, School of Chemistry and Biochemistry, Georgia Institute of Technology -- 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
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. anhp...@ou.edu 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! * 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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
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 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 timeensemble 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 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(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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 interface or send it to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Test Particle Insertion
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 j...@um.es
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 timeensemble 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
jalem...@vt.edu 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(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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
Re: [gmx-users] Test Particle Insertion
On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo j...@um.es 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 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 timeensemble 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 jalem...@vt.eduwrote:
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(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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
Re: [gmx-users] Test Particle Insertion
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 j...@um.es
mailto:j...@um.es 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 j...@um.es
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 timeensemble 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
jalem...@vt.edu 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
Re: [gmx-users] Test Particle Insertion
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 timeensemble 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 jalem...@vt.edu
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(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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 http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing list gmx-users@gromacs.org
mailto:gmx-users@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
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Re: [gmx-users] Test Particle Insertion
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul 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(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
--
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[gmx-users] Test Particle Insertion
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Test Particle Insertion
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(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@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!
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[gmx-users] Test Particle Insertion of Water
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 -- 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
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
Re: [gmx-users] Test Particle Insertion of Water
thank you Javier, I will try both in this case. On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo j...@um.es 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
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 V = -nan nm^3 mu = -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 j...@um.es 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
Re: [gmx-users] Test Particle Insertion of Water
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
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 j...@um.es 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://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_Listshttp://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
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 V = -nan nm^3 mu = -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 j...@um.es mailto:j...@um.es 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
Re: [gmx-users] Test Particle Insertion of Water
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 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 V = -nan nm^3 mu = -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 j...@um.es 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
Re: [gmx-users] Test Particle Insertion of Water
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 s.neuman...@gmail.comwrote: 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 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 V = -nan nm^3 mu = -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
Re: [gmx-users] Test Particle Insertion of Water
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 s.neuman...@gmail.com mailto:s.neuman...@gmail.com 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 j...@um.es 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 V =
Re: [gmx-users] Test Particle Insertion of Water
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 j...@um.es 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 s.neuman...@gmail.comwrote: 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 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 V = -nan nm^3 mu = -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
[gmx-users] Test particle insertion extra coordinate
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. -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4536816.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
RE: [gmx-users] test particle insertion with PME
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
RE: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
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 javascript:; 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 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 What can you do with the new Windows Live? Find out _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd1_052009___ 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
RE: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
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 javascript:; 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 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 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ 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
[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
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 _ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009___ 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
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 javascript:; 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 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
Re: [gmx-users] test particle insertion
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 ___ 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
