RE: [gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after

[Berk Hess]

Hi,

I tried to reproduce this, but I did not succeed.
mdrun always seems to write the correct z size in all output files.

Are you sure mdrun outputs a file (and which file, if so),
or is it another Gromacs program that produced the file with 0 z size?

You can simply manually correct the size in the file.
But please report back which program produced which incorrect file.

Berk

Date: Wed, 6 May 2009 00:39:18 +0800
From: crickzha...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] help: z-direction component of box vector becomes  0.0 
when using pdc = xy after

Hi, all
 
There are some things confusing and resulting in error when I run mdrun for 
energy minization and md.
 
I use Gromacs 4.0.4 to simulate electroosmotic flow in slab geometry with only 
2 dimensional 
periodic boundary (x and y), the system is aqueous solution with some ions, eg. 
CL- and Na+,
flowing through a plate channel, with external electrical field applied along 
x-direction, the height of channel
is z-direction. 
 
Coulomb interactions are computed with PME, and use pbc=xy, after running EM, 
all ouput tpr box sizes 
in z-direction becomes zero, eg. originally the box size is 
4.5,4.5,3.9, after EM, it became
4.5,4.5,0.0. so I can't use the output gro of EM for the MD run.
 
Did someone encounter this before and can give me some suggestion for my mdp 
setup?
 
Thanks in advance.
 
(sorry for bad English expressions)
 
some options for mdp file of mine are here:
 
pbc   = xy
rlist   = 1.1  
rcoulomb   = 1.1  
rvdw  = 1.1  
 
; electrostatics
coulombtype  = PME  
fourierspacing = 0.12
;fourier_nx  =  
;fourier_ny  =   
fourier_nz= 30
pme_order   = 4   
 dim
ewald_geometry  = 3dc   ; IMPORTANT
optimize_fft= yes   ; 
 
nwall = 2
wall_type   = 10-4
;wall_r_linpot  = 
wall_atomtype= SI  SI
wall_density   = 7.12 7.12

wall_ewald_zfac = 3
 
; NEMD
acc_grps= WA  WAb  WAu
accelerate  = 0.0 0.0 0.0  0.0 0.0 0.0  0.0 0.0 0.0
freezegrps  = WA  WAb  WAu
freezedim   = Y Y Y  Y Y Y  Y Y Y


; Electric fields 
E_x = 1 -0.55 0

 
Regards,
Yinhe Zhang

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[gmx-users] extending simulations

[Anna Marabotti]

Dear all,
I'd need to have a clarification about how to extend a simulation made using 
GROMACS 4 that has been
interrupted on a system due to walltime expiration. On the Wiki section I see:
"A simulation that has completed is extended using tpbconv, mdrun and 
checkpoint files (.cpt). A simulation
that has terminated, but not completed, due to e.g. the queue time ending, or 
better: the use of the -maxh
option of mdrun, can be continued without tpbconv. First the number of steps or 
time has to be changed in the
.tpr file, then the simulation is continued from the last checkpoint with 
mdrun. This will produce a binary
identical simulation that will be the same as it a continuous run was made.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"

If I understand well, the procedure using tpbconv should be applied only if I 
have finished my previous run
of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have to 
use tpbconv and then mdrun. On
the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only 
command I should provide is:

mdrun -s previous.tpr -cpi previous.cpt

without modifying the previous.tpr file.
Could you please confirm me about this point?
Many thanks and best regards
Anna

__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabo...@isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

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Re:[gmx-users] extending simulations

[zhang]

You can use the mdrun command:
How to restart a crashed run. The mdrun program now uses a very handy 
checkpointing feature.  
Restarting crashed runs is easy with mdrun. 
 
mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr –g prev.log –cpi -append




在2009-05-06，"Anna Marabotti"  写道：
>Dear all,
>I'd need to have a clarification about how to extend a simulation made using 
>GROMACS 4 that has been
>interrupted on a system due to walltime expiration. On the Wiki section I see:
>"A simulation that has completed is extended using tpbconv, mdrun and 
>checkpoint files (.cpt). A simulation
>that has terminated, but not completed, due to e.g. the queue time ending, or 
>better: the use of the -maxh
>option of mdrun, can be continued without tpbconv. First the number of steps 
>or time has to be changed in the
>.tpr file, then the simulation is continued from the last checkpoint with 
>mdrun. This will produce a binary
>identical simulation that will be the same as it a continuous run was made.
>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
>mdrun -s next.tpr -cpi previous.cpt"
>
>If I understand well, the procedure using tpbconv should be applied only if I 
>have finished my previous run
>of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have to 
>use tpbconv and then mdrun. On
>the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only 
>command I should provide is:
>
>mdrun -s previous.tpr -cpi previous.cpt
>
>without modifying the previous.tpr file.
>Could you please confirm me about this point?
>Many thanks and best regards
>Anna
>
>__
>Anna Marabotti, Ph.D.
>Laboratory of Bioinformatics and Computational Biology
>Institute of Food Science, CNR
>Via Roma 64
>83100 Avellino (Italy)
>Phone: +39 0825 299651
>Fax: +39 0825 781585
>Skype: annam1972
>E-mail: amarabo...@isa.cnr.it
>Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
>"If you think you are too small to make a difference, try sleeping with a 
>mosquito"
>
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Re: [gmx-users] extending simulations

[Justin A. Lemkul]

Anna Marabotti wrote:

Dear all,
I'd need to have a clarification about how to extend a simulation made using 
GROMACS 4 that has been
interrupted on a system due to walltime expiration. On the Wiki section I see:
"A simulation that has completed is extended using tpbconv, mdrun and 
checkpoint files (.cpt). A simulation
that has terminated, but not completed, due to e.g. the queue time ending, or 
better: the use of the -maxh
option of mdrun, can be continued without tpbconv. First the number of steps or 
time has to be changed in the
.tpr file, then the simulation is continued from the last checkpoint with 
mdrun. This will produce a binary
identical simulation that will be the same as it a continuous run was made.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"

If I understand well, the procedure using tpbconv should be applied only if I 
have finished my previous run
of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have to 
use tpbconv and then mdrun. On
the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only 
command I should provide is:

mdrun -s previous.tpr -cpi previous.cpt



Yes.  And the -append option, if you want to continue writing to the same output 
files, without having to use trjcat/eneconv later.


-Justin


without modifying the previous.tpr file.
Could you please confirm me about this point?
Many thanks and best regards
Anna

__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabo...@isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

"If you think you are too small to make a difference, try sleeping with a 
mosquito"

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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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Re: [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

[XAvier Periole]

Dear Dennis,

I believe your problem is due to the fact that when the  
autocorrelation is
done on a dihedral angle a cos function is used instead of the angle  
itself.
This is good to account for periodicity. This function is not  
implemented

in the -P 1 2 3 ... if I recall correctly.

I think you can get around it by giving the data (dihedral angles  
values)

to g_analyse and ask to do the autocorrelation. Or you can get into
autocorr.c and implement the function you'd need.

On May 5, 2009, at 11:58 PM, Dennis Glass wrote:



Hello,

I am facing a problem with g_angle. I want to analyse some  
dihedrals. When calculating the autocorrelation function, g_angle  
crashes if I want to use a Legendre polynomial for the ACF. Can I  
somehow handle this problem?



The command lines are below together with the error message. I am  
using version 4.0.4 of Gromacs. My indexfile contains 4 atoms.



DOES WORK:
g_angle -f run01-10.trr -oc dicorr -type dihedral -n myindexfile


DOES NOT WORK:
g_angle -f run01-10.trr -oc dicorr -type dihedral -n myindexfile -P  
1 [or 2, 3]

ERROR MESSAGE:
---
Program g_angle, VERSION 4.0.4
Source code file: autocorr.c, line: 607

Fatal error:
Incompatible options bCos && bVector (autocorr.c, 608)
---


Thanks for your help
Dennis

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[gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

[wuxiao]

Dear gmx users,

  I have performed NPT MD simulations and achieved a trr file. Now I want to 
start another NVT MD simulations using some frame as the initial configuration. 
But I was puzzled by how to abstract any frame from the trajectory file and to 
save it as a gro file. Please give me some hints. Thank you very much!

 

best regards,

xiaowu

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Re: [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

[David van der Spoel]

Dennis Glass wrote:


Hello,

I am facing a problem with g_angle. I want to analyse some dihedrals. 
When calculating the autocorrelation function, g_angle crashes if I want 
to use a Legendre polynomial for the ACF. Can I somehow handle this problem?




The legendre polynomial only applies to vectors, and given a dihedral
you have only a scalar value. You can apply a Legendre polynomial to
e.g. bonds, to obtain NH order parameters.

The command lines are below together with the error message. I am using 
version 4.0.4 of Gromacs. My indexfile contains 4 atoms.



DOES WORK:
g_angle -f run01-10.trr -oc dicorr -type dihedral -n myindexfile


DOES NOT WORK:
g_angle -f run01-10.trr -oc dicorr -type dihedral -n myindexfile -P 1 
[or 2, 3]

ERROR MESSAGE:
---
Program g_angle, VERSION 4.0.4
Source code file: autocorr.c, line: 607

Fatal error:
Incompatible options bCos && bVector (autocorr.c, 608)
---


Thanks for your help
Dennis




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Re: [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

[Justin A. Lemkul]

wuxiao wrote:
> Dear gmx users,
>   I have performed NPT MD simulations and achieved a trr file. Now I 
> want to start another NVT MD simulations using some frame as the initial 
> configuration. But I was puzzled by how to abstract any frame from the 
> trajectory file and to save it as a gro file. Please give me some hints. 
> Thank you very much!
>  

trjconv -dump

-Justin

> best regards,
> xiaowu
> 
> 
> 立即试试微软地图新功能，msn互动浏览！ 立刻体验！ 
> 
> 
> 
> 
> 
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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] problem with mpi

[jagannath mondal]

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed 
mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is 
very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi 
in background, the output log file cites following error:   "mpiexec_yethiraj22 
(handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect 
from /dev/null"3. The simulation also crashed citing error in the output log 
file: *** glibc detected *** mdrun_mpi: malloc(): memory corruption (fast): 
0x0c37ea90 ***.
Any help and suggestion in this regard will be highly 
appreciated.ThanksJagannath Mondal


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[gmx-users] Questions to pullx.xvg

[Thomas Schlesier]

Hi all,
what are the meanings of the columns X and dX? From the manual i think
the first column X should be the position of the pull-group. But in my
case it is the position of the reference group, so i'm a little bit
troubled. And what is dX? For me it looks that this is the vector from
the reference-group to the pull-group. And then the forces in pullf.xvg
were calculated with:
F(t)= k*[S - (RP(t)-RP(0))]
Where F is the force, S the vector from the reference-group to the
spring (= pull_init + t * pull_rate * pull_vec) and RP the vector from
the reference-group to the pull-group and t the time.
(I used the umbrella pulling, with pull-geometry = position)
Am i right?

Greetings Thomas
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RE: [gmx-users] Questions to pullx.xvg

[Berk Hess]

Hi,

You are completely right.
This should have been documented somewhere.
But I changed this after the 4.0 release in on of the minor releases,
therefore this could not be documented.
In pullx.xvg X 0 means the coordinate(s) of group 0 and dX 1 the vector
from group 0 to group 1.

Berk

> Date: Wed, 6 May 2009 10:56:29 +0200
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Questions to pullx.xvg
> 
> Hi all,
> what are the meanings of the columns X and dX? From the manual i think
> the first column X should be the position of the pull-group. But in my
> case it is the position of the reference group, so i'm a little bit
> troubled. And what is dX? For me it looks that this is the vector from
> the reference-group to the pull-group. And then the forces in pullf.xvg
> were calculated with:
> F(t)= k*[S - (RP(t)-RP(0))]
> Where F is the force, S the vector from the reference-group to the
> spring (= pull_init + t * pull_rate * pull_vec) and RP the vector from
> the reference-group to the pull-group and t the time.
> (I used the umbrella pulling, with pull-geometry = position)
> Am i right?
> 
> Greetings Thomas
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[gmx-users] mpi problem

[jagannath mondal]

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed 
mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is 
very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi 
in background, the output log file cites following error:   "mpiexec_yethiraj22 
(handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect 
from /dev/null"3. The simulation also crashed citing error in the output log 
file: *** glibc detected *** mdrun_mpi: malloc(): memory corruption (fast): 
0x0c37ea90 ***.
Any help and suggestion in this regard will be highly 
appreciated.ThanksJagannath Mondal


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Re: [gmx-users] g_angle - Order of Legendre polynomial for ACF - BUG ?

[David van der Spoel]

Dennis Glass wrote:


Hello,

I am facing a problem with g_angle. I want to analyse some dihedrals. 
When calculating the autocorrelation function, g_angle crashes if I want 
to use a Legendre polynomial for the ACF. Can I somehow handle this problem?



The legendre polynomial only applies to vectors, and given a dihedral 
you have only a scalar value. You can apply a Legendre polynomial to 
e.g. bonds, to obtain NH order parameters.


The command lines are below together with the error message. I am using 
version 4.0.4 of Gromacs. My indexfile contains 4 atoms.



DOES WORK:
g_angle -f run01-10.trr -oc dicorr -type dihedral -n myindexfile


DOES NOT WORK:
g_angle -f run01-10.trr -oc dicorr -type dihedral -n myindexfile -P 1 
[or 2, 3]

ERROR MESSAGE:
---
Program g_angle, VERSION 4.0.4
Source code file: autocorr.c, line: 607

Fatal error:
Incompatible options bCos && bVector (autocorr.c, 608)
---


Thanks for your help
Dennis




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] How to concatenate several input trajector y files in sorted order in GMX4.01

[zhang]

Dear all:
I extended a mdrun in GMX4.01,and the two trajectory files can not been 
concatenated,i.e.the "trjcat"command is invalid in GMX4.01. How to solve this 
question?
Thank you very much!
Sincerely 

 
Zhang,Rui
ShanDong university___
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Re: [gmx-users] How to concatenate severa l input trajectory files in sorted order in GM X4.01

[Justin A. Lemkul]

zhang wrote:


Dear all:
I extended a mdrun in GMX4.01,and the two trajectory files can not been 
concatenated,i.e.the "trjcat"command is invalid in GMX4.01. How to solve 
this question?


Do not use 4.0.1; it was inadvertently crippled during development.  Upgrade to 
4.0.4 and start over.


-Justin


Thank you very much!
Sincerely
 
Zhang,Rui

ShanDong university



穿越地震带 纪念汶川地震一周年 






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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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RE: [gmx-users] Questions to pullx.xvg

[Thomas Schlesier]

Hi,
thanks for the clarification.
Thomas

> 
> 
> Hi,
> 
> You are completely right.
> This should have been documented somewhere.
> But I changed this after the 4.0 release in on of the minor releases,
> therefore this could not be documented.
> In pullx.xvg X 0 means the coordinate(s) of group 0 and dX 1 the vector
> from group 0 to group 1.
> 
> Berk
> 
>> Date: Wed, 6 May 2009 10:56:29 +0200
>> From: schl...@uni-mainz.de
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] Questions to pullx.xvg
>>
>> Hi all,
>> what are the meanings of the columns X and dX? From the manual i think
>> the first column X should be the position of the pull-group. But in my
>> case it is the position of the reference group, so i'm a little bit
>> troubled. And what is dX? For me it looks that this is the vector from
>> the reference-group to the pull-group. And then the forces in pullf.xvg
>> were calculated with:
>> F(t)= k*[S - (RP(t)-RP(0))]
>> Where F is the force, S the vector from the reference-group to the
>> spring (= pull_init + t * pull_rate * pull_vec) and RP the vector from
>> the reference-group to the pull-group and t the time.
>> (I used the umbrella pulling, with pull-geometry = position)
>> Am i right?
>>
>> Greetings Thomas
>> ___
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RE: [gmx-users] extending simulations

[kyungchan chae]

If you want to extend your simulation, simply use the 'append' command.

: mdrun -append yes -cpi state.cpt

Extending a simulation is quite simple. However, if your trajectory file is
larger than 2GB, you are going to have a problem. I tested it a few weeks
ago and found out that the 'append' option only worked when the size of
trajectory file is smaller than 2GB. I reported this issue to Gromacs
bugzilla(#315). Please check my bug report. I really hope to share
information about this issue.



-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Anna Marabotti
Sent: Wednesday, May 06, 2009 8:31 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] extending simulations

Dear all,
I'd need to have a clarification about how to extend a simulation made using
GROMACS 4 that has been
interrupted on a system due to walltime expiration. On the Wiki section I
see:
"A simulation that has completed is extended using tpbconv, mdrun and
checkpoint files (.cpt). A simulation
that has terminated, but not completed, due to e.g. the queue time ending,
or better: the use of the -maxh
option of mdrun, can be continued without tpbconv. First the number of steps
or time has to be changed in the
.tpr file, then the simulation is continued from the last checkpoint with
mdrun. This will produce a binary
identical simulation that will be the same as it a continuous run was made.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"

If I understand well, the procedure using tpbconv should be applied only if
I have finished my previous run
of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have
to use tpbconv and then mdrun. On
the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only
command I should provide is:

mdrun -s previous.tpr -cpi previous.cpt

without modifying the previous.tpr file.
Could you please confirm me about this point?
Many thanks and best regards
Anna

__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabo...@isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

"If you think you are too small to make a difference, try sleeping with a
mosquito"

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RE: [gmx-users] extending simulations

[vidhya sankar]

dear sir/Madam  
i want to work in mopac/gromacs interface for that i have downloaded mopac 
7-1.10 tar.gz when run ./configure in the TAR file in command  prompt of redhat 
linux EL5 to install mopac 
 i got the the following error in command prompt 
bash: ./configure: /bin/sh^M: bad interpreter: No such file or directory 
 please kindly rectify the error in the configure file i am waiting for  your 
reply
thanks in Advance
 
 
 
 
 
 
 
 
 


--- On Wed, 6/5/09, kyungchan chae  wrote:


From: kyungchan chae 
Subject: RE: [gmx-users] extending simulations
To: "'Discussion list for GROMACS users'" 
Date: Wednesday, 6 May, 2009, 8:02 PM


If you want to extend your simulation, simply use the 'append' command.

: mdrun -append yes -cpi state.cpt

Extending a simulation is quite simple. However, if your trajectory file is
larger than 2GB, you are going to have a problem. I tested it a few weeks
ago and found out that the 'append' option only worked when the size of
trajectory file is smaller than 2GB. I reported this issue to Gromacs
bugzilla(#315). Please check my bug report. I really hope to share
information about this issue.



-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Anna Marabotti
Sent: Wednesday, May 06, 2009 8:31 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] extending simulations

Dear all,
I'd need to have a clarification about how to extend a simulation made using
GROMACS 4 that has been
interrupted on a system due to walltime expiration. On the Wiki section I
see:
"A simulation that has completed is extended using tpbconv, mdrun and
checkpoint files (.cpt). A simulation
that has terminated, but not completed, due to e.g. the queue time ending,
or better: the use of the -maxh
option of mdrun, can be continued without tpbconv. First the number of steps
or time has to be changed in the
..tpr file, then the simulation is continued from the last checkpoint with
mdrun. This will produce a binary
identical simulation that will be the same as it a continuous run was made.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"

If I understand well, the procedure using tpbconv should be applied only if
I have finished my previous run
of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have
to use tpbconv and then mdrun. On
the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only
command I should provide is:

mdrun -s previous.tpr -cpi previous.cpt

without modifying the previous.tpr file.
Could you please confirm me about this point?
Many thanks and best regards
Anna

__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabo...@isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

"If you think you are too small to make a difference, try sleeping with a
mosquito"

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  Bollywood news, movie reviews, film trailers and more! Go to 
http://in.movies.yahoo.com/___
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Re: [gmx-users] extending simulations

[Justin A. Lemkul]

Please start a new thread if you are asking a new question; it will help get the 
attention of someone who may be interested in helping you, but who may not have 
any comments on the "extending simulations" thread.


vidhya sankar wrote:
dear sir/Madam  

i want to work in mopac/gromacs interface for that i have downloaded 
mopac 7-1.10 tar.gz when run ./configure in the TAR file in command  
prompt of redhat linux EL5 to install mopac


 i got the the following error in command prompt

*bash: ./configure: /bin/sh^M: bad interpreter: No such file or directory*



The configure file has been modified by an editor that has left hidden 
characters (^M) at the end of lines.  You may need to run something like 
dos2unix on the file, or at least explore it (and perhaps others) with a plain 
text editor like vi or emacs.


-Justin

 please kindly rectify the error in the configure file i am waiting for  
your reply


thanks in Advance
 
 
 
 
 
 
 
 
 



--- On *Wed, 6/5/09, kyungchan chae //* wrote:


From: kyungchan chae 
Subject: RE: [gmx-users] extending simulations
To: "'Discussion list for GROMACS users'" 
Date: Wednesday, 6 May, 2009, 8:02 PM

If you want to extend your simulation, simply use the 'append' command.

: mdrun -append yes -cpi state.cpt

Extending a simulation is quite simple. However, if your trajectory
file is
larger than 2GB, you are going to have a problem. I tested it a few
weeks
ago and found out that the 'append' option only worked when the size of
trajectory file is smaller than 2GB. I reported this issue to Gromacs
bugzilla(#315). Please check my bug report. I really hope to share
information about this issue.



-Original Message-
From: gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org

]
On Behalf Of Anna Marabotti
Sent: Wednesday, May 06, 2009 8:31 AM
To: gmx-users@gromacs.org

Subject: [gmx-users] extending simulations

Dear all,
I'd need to have a clarification about how to extend a simulation
made using
GROMACS 4 that has been
interrupted on a system due to walltime expiration. On the Wiki
section I
see:
"A simulation that has completed is extended using tpbconv, mdrun and
checkpoint files (.cpt). A simulation
that has terminated, but not completed, due to e.g. the queue time
ending,
or better: the use of the -maxh
option of mdrun, can be continued without tpbconv. First the number
of steps
or time has to be changed in the
.tpr file, then the simulation is continued from the last checkpoint
with
mdrun. This will produce a binary
identical simulation that will be the same as it a continuous run
was made.
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"

If I understand well, the procedure using tpbconv should be applied
only if
I have finished my previous run
of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case
I have
to use tpbconv and then mdrun. On
the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns,
the only
command I should provide is:

mdrun -s previous.tpr -cpi previous.cpt

without modifying the previous.tpr file.
Could you please confirm me about this point?
Many thanks and best regards
Anna

__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabo...@isa.cnr.it

Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm

"If you think you are too small to make a difference, try sleeping
with a
mosquito"

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..
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[gmx-users] problem with particle decomposition in gromacs 4.0.4

[Suman Chakrabarty]

Hi,

I am trying particle decomposition with gromacs 4.0.4 for a small
polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at
the very beginning without any useful error message, when I use
version 4.0.4 with option -pd. Whereas everything remaining same it's
still running fine in version 3.3.3. I have tried 4, 8, 16 nodes with
the same result. How do I troubleshoot this? I need to use the
particle decomposition method since the PLUMED plugin to perform
metadynamics supports only pd as of now.

Here are the last few lines from the log, stderr and stdout files:

log:

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
  --- Thank You ---  
==

stderr:
==
Getting Loaded...
Reading file c20.G53a6.eq.gmx404.tpr, VERSION 4.0.4 (single precision)
Loaded with Money

starting mdrun 'Protein in water'
250 steps,   5000.0 ps.
===

stdout:
===
/opt/gridengine/default/spool/compute-0-4/active_jobs/5329.1/pe_hostfile
ibc4
ibc4
ibc4
ibc4
rank 2 in job 1  compute-0-4.local_46551   caused collective abort of all ranks
  exit status of rank 2: killed by signal 9
rank 1 in job 1  compute-0-4.local_46551   caused collective abort of all ranks
  exit status of rank 1: killed by signal 9
=

Thanks for any suggestion.


Best regards,
Suman.
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RE: [gmx-users] problem with particle decomposition in gromacs 4.0.4

[Berk Hess]

Hi,

Are the crashes with plain 4.0.4, or 4.0.4 with PLUMED?
I have not heard of crashes in 4.0.4 with particle decomposition,
so it might have to do with the link with PLUMED.

Have you tried running 4.0.4 in single processor?

If plain Gromacs 4.0.4 crahes on your system with PD,
please file a report on bugzilla.gromacs.org and attach the tpr file.

Berk

> Date: Wed, 6 May 2009 20:23:56 +0530
> From: su...@sscu.iisc.ernet.in
> To: gmx-users@gromacs.org
> Subject: [gmx-users] problem with particle decomposition in gromacs 4.0.4
> 
> Hi,
> 
> I am trying particle decomposition with gromacs 4.0.4 for a small
> polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at
> the very beginning without any useful error message, when I use
> version 4.0.4 with option -pd. Whereas everything remaining same it's
> still running fine in version 3.3.3. I have tried 4, 8, 16 nodes with
> the same result. How do I troubleshoot this? I need to use the
> particle decomposition method since the PLUMED plugin to perform
> metadynamics supports only pd as of now.
> 
> Here are the last few lines from the log, stderr and stdout files:
> 
> log:
> 
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  rest
> 
>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
>   --- Thank You ---  
> ==
> 
> stderr:
> ==
> Getting Loaded...
> Reading file c20.G53a6.eq.gmx404.tpr, VERSION 4.0.4 (single precision)
> Loaded with Money
> 
> starting mdrun 'Protein in water'
> 250 steps,   5000.0 ps.
> ===
> 
> stdout:
> ===
> /opt/gridengine/default/spool/compute-0-4/active_jobs/5329.1/pe_hostfile
> ibc4
> ibc4
> ibc4
> ibc4
> rank 2 in job 1  compute-0-4.local_46551   caused collective abort of all 
> ranks
>   exit status of rank 2: killed by signal 9
> rank 1 in job 1  compute-0-4.local_46551   caused collective abort of all 
> ranks
>   exit status of rank 1: killed by signal 9
> =
> 
> Thanks for any suggestion.
> 
> 
> Best regards,
> Suman.
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[gmx-users] Martini+elastic network

[Enrico Spiga]

Dear all,
I am trying to run an energy minimization of a protein using Martini model +
Elastic Network.
I created correctly the itp file adding the constrain for the elastic
network.

when I try to submit the job on 32 processors I get the following:


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Re: [gmx-users] Martini+elastic network

[Justin A. Lemkul]

Enrico Spiga wrote:
Dear all, 

I am trying to run an energy minimization of a protein using Martini 
model + Elastic Network.
I created correctly the itp file adding the constrain for the elastic 
network.


when I try to submit the job on 32 processors I get the following:


the given box and a minimum cell size of 3.4336 nm



First, upgrade to the most current version (4.0.4) - it contains many 
improvements and bugfixes.


Second, take the advice mdrun is giving you.  Your system cannot be split into 
32 pieces.  Either change the desired number of processors, or modify the 
options mdrun has indicated.  More information is availabe in the manual, the 
Gromacs 4 paper, and in the list archive, as this problem has been raised before.


-Justin



Thank you very much in advance


--
Enrico

Reality is that wich, when you stop believing in it, doesn't go away.
Philip K. Dick

--




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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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RE: [gmx-users] problem with particle decomposition in gromacs 4.0.4

[Suman Chakrabarty]

Yes, I have encountered this crash with plain Gromacs 4.0.4 as well. I 
have not tried single processor, but with domain decomposition it runs 
fine. I am not sure whether it has got to do anything with our parallel 
architecture though.


In any case, I shall file a report after I reproduce this for a few 
slightly different systems.



Regards,
Suman.


On Wed, 6 May 2009, Berk Hess wrote:



Hi,

Are the crashes with plain 4.0.4, or 4.0.4 with PLUMED?
I have not heard of crashes in 4.0.4 with particle decomposition,
so it might have to do with the link with PLUMED.

Have you tried running 4.0.4 in single processor?

If plain Gromacs 4.0.4 crahes on your system with PD,
please file a report on bugzilla.gromacs.org and attach the tpr file.

Berk


Date: Wed, 6 May 2009 20:23:56 +0530
From: su...@sscu.iisc.ernet.in
To: gmx-users@gromacs.org
Subject: [gmx-users] problem with particle decomposition in gromacs 4.0.4

Hi,

I am trying particle decomposition with gromacs 4.0.4 for a small
polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at
the very beginning without any useful error message, when I use
version 4.0.4 with option -pd. Whereas everything remaining same it's
still running fine in version 3.3.3. I have tried 4, 8, 16 nodes with
the same result. How do I troubleshoot this? I need to use the
particle decomposition method since the PLUMED plugin to perform
metadynamics supports only pd as of now.

Here are the last few lines from the log, stderr and stdout files:

log:

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
  --- Thank You ---  
==

stderr:
==
Getting Loaded...
Reading file c20.G53a6.eq.gmx404.tpr, VERSION 4.0.4 (single precision)
Loaded with Money

starting mdrun 'Protein in water'
250 steps,   5000.0 ps.
===

stdout:
===
/opt/gridengine/default/spool/compute-0-4/active_jobs/5329.1/pe_hostfile
ibc4
ibc4
ibc4
ibc4
rank 2 in job 1  compute-0-4.local_46551   caused collective abort of all ranks
  exit status of rank 2: killed by signal 9
rank 1 in job 1  compute-0-4.local_46551   caused collective abort of all ranks
  exit status of rank 1: killed by signal 9
=

Thanks for any suggestion.


Best regards,
Suman.


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[gmx-users] P-coupling in vacuum, inflexibility

[Pavel Semenyuk]

Dear colleagues,

I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for 
it a very
big box, put my molecules into this box (without water) and then do simulations 
with
pressure coupling to make my box smaller. So, how can I make my molecules 
inflexible? if
I set links or shake constraints, it results too many warnings ("Warning: 1-4
interaction between 12 and 33 at distance 30.841 which is larger than the 1-4 
table size
2.400 nm").
Thank you...

Best regards,
Pavel I. Semenyuk

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Re: [gmx-users] P-coupling in vacuum, inflexibility

[Tsjerk Wassenaar]

Hi Pavel,

It seems that your molecules are broken over the periodic boundaries.
Make sure that you set up your coordinates and topology file
correctly.

Cheers,

Tsjerk

2009/5/6 Pavel Semenyuk :
> Dear colleagues,
>
> I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for 
> it a very
> big box, put my molecules into this box (without water) and then do 
> simulations with
> pressure coupling to make my box smaller. So, how can I make my molecules 
> inflexible? if
> I set links or shake constraints, it results too many warnings ("Warning: 1-4
> interaction between 12 and 33 at distance 30.841 which is larger than the 1-4 
> table size
> 2.400 nm").
> Thank you...
>
> Best regards,
> Pavel I. Semenyuk
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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[gmx-users] Energy minimization error by GMX 4.0.4

[Yanmei Song]

 Dear All:

I just installed the gmx_4.0.4 double precision.

When I do EM, the grompp_d command has no problem. However after I submit
the job, it gives me the following error. Anyone can tell me what is the
problem which may cause that? By the way, in 4.0.4, it can only use 4 CPU,
right? Can we still specify how much CPU we want to use by -np?

Reading file /home/ysong30/pdm80/em.tpr, VERSION 4.0.4 (double precision)

---
Program mdrun, VERSION 3.3.3
Source code file: tpxio.c, line: 1192

Fatal error:
reading tpx file (/home/ysong30/pdm80/em.tpr) version 58 with version 40
program


-- 
Yanmei Song
Department of Chemical Engineering
ASU
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[gmx-users] Re: Energy minimization error by GMX 4.0.4

[Yanmei Song]

Also I have checked that it works well in gmx_3.3.3. Anyone can tell me what
is the problem ?  Thanks!

On Wed, May 6, 2009 at 1:47 PM, Yanmei Song  wrote:

> Dear All:
>
> I just installed the gmx_4.0.4 double precision.
>
> When I do EM, the grompp_d command has no problem. However after I submit
> the job, it gives me the following error. Anyone can tell me what is the
> problem which may cause that? By the way, in 4.0.4, it can only use 4 CPU,
> right? Can we still specify how much CPU we want to use by -np?
>
> Reading file /home/ysong30/pdm80/em.tpr, VERSION 4.0.4 (double precision)
>
> ---
> Program mdrun, VERSION 3.3.3
> Source code file: tpxio.c, line: 1192
>
> Fatal error:
> reading tpx file (/home/ysong30/pdm80/em.tpr) version 58 with version 40
> program
>
>
> --
> Yanmei Song
> Department of Chemical Engineering
> ASU
>



-- 
Yanmei Song
Department of Chemical Engineering
ASU
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Re: [gmx-users] Energy minimization error by GMX 4.0.4

[Justin A. Lemkul]

Yanmei Song wrote:

  Dear All:

I just installed the gmx_4.0.4 double precision.

When I do EM, the grompp_d command has no problem. However after I 
submit the job, it gives me the following error. Anyone can tell me what 
is the problem which may cause that? By the way, in 4.0.4, it can only 
use 4 CPU, right? Can we still specify how much CPU we want to use by -np?


Reading file /home/ysong30/pdm80/em.tpr, VERSION 4.0.4 (double precision)

---
Program mdrun, VERSION 3.3.3
Source code file: tpxio.c, line: 1192

Fatal error:
reading tpx file (/home/ysong30/pdm80/em.tpr) version 58 with version 40 
program




You cannot use a 4.0.4-generated .tpr file with software version 3.3.3; many 
features present in 4.0.x are incompatible with an older version.  Always be 
consistent!


-Justin



--
Yanmei Song
Department of Chemical Engineering
ASU




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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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Re: [gmx-users] Energy minimization error by GMX 4.0.4

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Yanmei Song wrote:

  Dear All:

I just installed the gmx_4.0.4 double precision.

When I do EM, the grompp_d command has no problem. However after I 
submit the job, it gives me the following error. Anyone can tell me 
what is the problem which may cause that? By the way, in 4.0.4, it can 
only use 4 CPU, right? Can we still specify how much CPU we want to 
use by -np?




And yes, -np can use however many processors you would like to use (provided the 
domain decomposition can be established on that number of nodes).



Reading file /home/ysong30/pdm80/em.tpr, VERSION 4.0.4 (double precision)

---
Program mdrun, VERSION 3.3.3
Source code file: tpxio.c, line: 1192

Fatal error:
reading tpx file (/home/ysong30/pdm80/em.tpr) version 58 with version 
40 program




You cannot use a 4.0.4-generated .tpr file with software version 3.3.3; 
many features present in 4.0.x are incompatible with an older version.  
Always be consistent!


-Justin



--
Yanmei Song
Department of Chemical Engineering
ASU




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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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Re: [gmx-users] Energy minimization error by GMX 4.0.4

[Mark Abraham]

Yanmei Song wrote:

  Dear All:

I just installed the gmx_4.0.4 double precision.

When I do EM, the grompp_d command has no problem. However after I 
submit the job, it gives me the following error. Anyone can tell me what 
is the problem which may cause that? 


You're using a new .tpr with an old mdrun.

By the way, in 4.0.4, it can only 
use 4 CPU, right? 


No.


Can we still specify how much CPU we want to use by -np?


As an argument to mdrun yes, as an argument to grompp, no.

Mark
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Re: [gmx-users] problem with mpi

[Mark Abraham]

jagannath mondal wrote:

Hi,
I am trying to use parallel gromacs3.3.3  mdrun programme  .I have 
installed mpich2 in our quadcore machine. But I am having 3 problems:

   1. The scaling is very poor among 4 cores: varies between 30-70 %.
2. If I run the mdrun_mpi in background, the output log file cites 
following error: 
  "mpiexec_yethiraj22 (handle_stdin_input 1089): stdin problem; if pgm 
is run in background, redirect from /dev/null"
3. The simulation also crashed citing error in the output log file: *** 
glibc detected *** mdrun_mpi: malloc(): memory corruption (fast): 
0x0c37ea90 ***.


Unless you actually need 3.3.3 for some scientific reason, go and 
install 4.0.4. Otherwise, you seem to have some kind of broken/ancient 
MPI installation that also might need an update.


Mark
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Re: [gmx-users] Energy minimization error by GMX 4.0.4

[Yanmei Song]

Thank you so much for all the helpful response.

On Wed, May 6, 2009 at 4:59 PM, Mark Abraham wrote:

> Yanmei Song wrote:
>
>>  Dear All:
>>
>> I just installed the gmx_4.0.4 double precision.
>>
>> When I do EM, the grompp_d command has no problem. However after I submit
>> the job, it gives me the following error. Anyone can tell me what is the
>> problem which may cause that?
>>
>
> You're using a new .tpr with an old mdrun.
>
>  By the way, in 4.0.4, it can only use 4 CPU, right?
>>
>
> No.
>
>  Can we still specify how much CPU we want to use by -np?
>>
>
> As an argument to mdrun yes, as an argument to grompp, no.
>
> Mark
>
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>



-- 
Yanmei Song
Department of Chemical Engineering
ASU
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[gmx-users] modify lennard jones parameters to time-dependent

[Xinghua Shi]

Dear all,

Is there any way to modify the LJ potential as a time dependent value,
e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is
time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to
be modified, which C file should I find?

Xinghua
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Re: [gmx-users] modify lennard jones parameters to time-dependent

[Mark Abraham]

Xinghua Shi wrote:

Dear all,

Is there any way to modify the LJ potential as a time dependent value,
e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is
time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to
be modified, which C file should I find?


Simplest would be to generate a series of suitable LJ tables and pass 
the correct table to the non-bonded kernel to use for the table lookups, 
however that will be slower than computed LJ. Otherwise, you have to 
modify the non-bonded kernels. There's a spare parameter you can use to 
pass in the current value of e(t). Search the mailing list for advice on 
modifying non-bonded kernels - I've given some before.


Mark
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[gmx-users] itp and gro files

[Payman Pirzadeh]

I was wondering if the order of sites in .gro file should be the same as in
.itp file.

 

Payman

 

 

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Re: [gmx-users] itp and gro files

[Justin A. Lemkul]

Payman Pirzadeh wrote:
I was wondering if the order of sites in .gro file should be the same as 
in .itp file.


 


Yes, otherwise, you will see grompp warnings indicating that atom names in the 
.top and .gro do not match.


-Justin



Payman

 

 





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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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RE: [gmx-users] itp and gro files

[Payman Pirzadeh]

Thank you very much.

Payman

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: May 6, 2009 8:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] itp and gro files



Payman Pirzadeh wrote:
> I was wondering if the order of sites in .gro file should be the same as 
> in .itp file.
> 
>  

Yes, otherwise, you will see grompp warnings indicating that atom names in
the 
.top and .gro do not match.

-Justin

> 
> Payman
> 
>  
> 
>  
> 
> 
> 
> 
> ___
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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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RE: [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

[Cheong Wee Loong, Daniel]

You can use trjconv to extract a frame from the trajectory, e.g.

trjconv �Cf xxx.trr �Co xxx.gro �Cb ttt �Ce ttt






From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of wuxiao
Sent: Wednesday, May 06, 2009 8:42 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Can we abstract any frame from the trajectory file(trr) 
and save it as a gro file?

Dear gmx users,
  I have performed NPT MD simulations and achieved a trr file. Now I want to 
start another NVT MD simulations using some frame as the initial configuration. 
But I was puzzled by how to abstract any frame from the trajectory file and to 
save it as a gro file. Please give me some hints. Thank you very much!

best regards,
xiaowu

立即试试微软地图新功能，msn互动浏览！ 立刻体验！


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Re: [gmx-users] modify lennard jones parameters to time-dependent

[David van der Spoel]

Mark Abraham wrote:

Xinghua Shi wrote:

Dear all,

Is there any way to modify the LJ potential as a time dependent value,
e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is
time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to
be modified, which C file should I find?


In your example you would also change the sign of the potential, which 
might give interesting effects.


However you can also use external forces using the accelaration options 
in the mdp file, which might not be what you want though.




Simplest would be to generate a series of suitable LJ tables and pass 
the correct table to the non-bonded kernel to use for the table lookups, 
however that will be slower than computed LJ. Otherwise, you have to 
modify the non-bonded kernels. There's a spare parameter you can use to 
pass in the current value of e(t). Search the mailing list for advice on 
modifying non-bonded kernels - I've given some before.


Mark
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David.

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