[gmx-users] Re: Some questions on Tabulated Dihedral Potential
Hi Cynthia, I'm also working on including some tabulated functions but I don't have any simulation yet. Thus I'm not a 'specialist' in this topic, but I hope I can help you a little. Dear all, I tried to include 2 tabulated dihedral potential functions into my simulation. But it seems to be not able to generate correct results. The system just exploded. I defined 3601 points in each table (from -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two warning information: WARNING: For the 3598 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential WARNING: For the 3598 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential Do these two warnings matter very much? I checked the values for x,f(x),-f'(x) in the tables and don't think there're mistakes. has anyone of you met with such problems? There're also some other confusions: 1. Can the constant k before the cubic spline function be defined arbitrarily, as long as themultiplicationof k and f(x) equals to the dihedral potential? 2. The tables do not need to be supplied to mdrun using '-tableb', right? I found if I omitted -tableb and the following table files, GROMACS can still go and find the two tables. 3. how to use '-tableb' if two tables are supplied? '-tableb table_d1.xvg table_d2.xvg' or '-tableb table_d1.xvg -tableb table_d2.xvg'? I tried both and error information was given that GROMACS can not find 'table_d1_d1.xvg'. I then delete '_d1' in both of the commands and there was no error information any more. It seems that only one table can be supplied to mdrun by using'-tableb', the second table can not be recognized all the time. If you read the manual page of mdrun (i.e. in the appendix of GROMACS manual) you find the following: "When tabulated bonded functions are present in the topology, interaction functions are read using the -tableb option. For each different tabulated interaction type the table file name is modified in a different way: before the file extension an underscore is appended, then a b for bonds, an a for angles or a d for dihedrals and finally the table number of the interaction type." Thus you run mdrun -tableb mytablefilename.xvg and GROMACS automatically adds _d* before .xvg, where * is the table number specified in the topology. In your case GROMACS finds your table files automatically, because you gave them the default names GROMACS searches for. For further informations read chapters 4.2.13, 5.7.1 and D.74 (manpage mdrun) of the GROMACS manual. Thanks for your help CH Johannes ___ 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] Re: Some questions on Tabulated Dihedral Potential
Hi, Johannes Kamp wrote: Hi Cynthia, I'm also working on including some tabulated functions but I don't have any simulation yet. Thus I'm not a 'specialist' in this topic, but I hope I can help you a little. Dear all, I tried to include 2 tabulated dihedral potential functions into my simulation. But it seems to be not able to generate correct results. The system just exploded. I defined 3601 points in each table (from -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two warning information: WARNING: For the 3598 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential WARNING: For the 3598 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential Do these two warnings matter very much? I checked the values for x,f(x),-f'(x) in the tables and don't think there're mistakes. has anyone of you met with such problems? In the tables you should supply potentials and forces. The forces are also calculated numerically, and a warning is emitted if the numerical derivatives deviate too much from the forces supplied by the user. Since the forces are interpolated, if the numerical derivative is too far from the input what you'd get will be different then expected. You can calculate the derivatives yourself and see where there are deviations. Good luck, Ran ___ 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] Re: mdrun -nosum still complains that 15 % of the runtime was spent communicating energies
Thanks mark, I'll respond inline.
Chris Neale wrote:
I have now tested with and without -nosum and it appears that the option
is working (see 51 vs. 501 Number of communications) but that the total
amount of time communicating energies didn't go down by very much. Seems
strange to me. Anybody have any ideas if this is normal?
Seems strange, but perhaps a 45-second test is not sufficiently long to
demonstrate suitable scaling.
Agreed, although I find it a good jumping off point, especially now
that we need to optimize -npme. If I use quick tests to narrow down
the range of nodes/npme that is going to scale the best then I fine
tune it with longer scaling tests.
There's no discussion in the 4.0.5 release
notes of a relevant change to -nosum, but there has been a change:
http://oldwww.gromacs.org/content/view/181/132/.
Thanks, I did see this but don't think that it is related to this
issue, which I have now confirmed in both 4.0.4 and 4.0.5.
At the very least, I suggest adding an if statement to mdrun so that it
doesn't output the -nosum usage note if the user did in fact use -nosum
in that run.
Without using -nosum:
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 %
---
...
Write traj. 256 2 233.218 93.7 0.5
Update 256501 777.511 312.5 1.7
Constraints 256 1002 1203.894 483.9 2.7
Comm. energies 256501 7397.995 2973.916.5
Rest 256 128.058 51.5 0.3
---
Total384 44897.46818048.0 100.0
---
NOTE: 16 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 47.000 47.000100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 13485.788712.634 1.842 13.029
Finished mdrun on node 0 Mon Jul 20 12:53:41 2009
#
And using -nosum:
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 %
---
...
Write traj. 256 2 213.521 83.3 0.5
Update 256501 776.606 303.0 1.8
Constraints 256 1002 1200.285 468.2 2.7
Comm. energies 256 51 6926.667 2702.115.6
Rest 256 127.503 49.7 0.3
---
Total384 44296.67017280.0 100.0
---
NOTE: 16 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 45.000 45.000100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 14084.547744.277 1.924 12.475
#
Thanks,
Chris.
Chris Neale wrote:
Hello,
I have been running simulations on a larger number of processors
recently and am confused about the message regarding -nosum that
occurs at the end of the .log file. In this case, I have included the
-nosum option to mdrun and I still get this warning (gromacs 4.0.4).
My command was:
mpirun -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -machinefile
$PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.4/exec/bin/mdrun
-deffnm test -nosum -npme 128
Perhaps assigning the result of this to a variable and printing it
before executing it would help confirm that -nosum really was there.
I am not sure what you mean... the while line as a variable? I'm
pretty sure that -nosum is there.
Your mdrun output from your first email was...
#
To confirm that I am asking mdrun for -nosum, to stderr I get:
...
Option Type Value Description
--
-[no]h bool no Print help info and quit
-niceint0 Set the nicelevel
-deffnm string testSet the default filename for all file options
-[no]xvgrbool yes Add specific codes (legends etc.) in the
output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npmeint128 Number of separate nodes to be used for
PME, -1
回复： [gmx-users] Re: Some questions on T abulated Dihedral Potential
Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH 发件人： Ran Friedman r.fried...@bioc.uzh.ch 收件人： Discussion list for GROMACS users gmx-users@gromacs.org 已发送： 2009/7/21(周二), 上午8:17:11 主题： Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential Hi, Johannes Kamp wrote: Hi Cynthia, I'm also working on including some tabulated functions but I don't have any simulation yet. Thus I'm not a 'specialist' in this topic, but I hope I can help you a little. Dear all, I tried to include 2 tabulated dihedral potential functions into my simulation. But it seems to be not able to generate correct results. The system just exploded. I defined 3601 points in each table (from -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two warning information: WARNING: For the 3598 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential WARNING: For the 3598 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential Do these two warnings matter very much? I checked the values for x,f(x),-f'(x) in the tables and don't think there're mistakes. has anyone of you met with such problems? In the tables you should supply potentials and forces. The forces are also calculated numerically, and a warning is emitted if the numerical derivatives deviate too much from the forces supplied by the user. Since the forces are interpolated, if the numerical derivative is too far from the input what you'd get will be different then expected. You can calculate the derivatives yourself and see where there are deviations. Good luck, Ran ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/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: 回复： [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential
Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote: Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH ___ 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: 回复： [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential
Ran Friedman wrote: Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX Correction: der = (y[N+1] - y[N-1]) * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote: Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH ___ 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 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ 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] large force on an atom
hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using inflategro perl script. just after the first run when i'm running grompp to minimize it i have found a large force on a phenylalanin atom which is well over 1015 Now what to do with this one? I had a view of that particular atom through pymol which is an Oxygen (CO). Right now I’m a little anxious that if I keep this and go on it’ll affect the future steps. Any suggestions regarding this will be very encouraging. Thank You Shamik Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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] large force on an atom
Samik Bhattacharya wrote: hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using inflategro perl script. just after the first run when i'm running grompp to minimize it i have found a large force on a phenylalanin atom which is well over 10^15 ^ Now what to do with this one? I had a view of that particular atom through pymol which is an Oxygen (CO). Right now I’m a little anxious that if I keep this and go on it’ll affect the future steps. Any suggestions regarding this will be very encouraging.. Well, is that atom clashing with something else in your system? The only way I can think to get a force of 10^15 is substantial atomic overlap. -Justin Thank You Shamik Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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: 回复： 回复： [gmx-users] Re: So me questions on Tabulated Dihedral Potential
As I wrote it der is the derivative itself, so you should plot (-1)*der. Ran. hong bingbing wrote: Thanks Ran. Should there also be a minus sign before (y[N+1]-y[N-1]) because the third column in the table is -f'(x)? CH *发件人：* Ran Friedman r.fried...@bioc.uzh.ch *收件人：* Discussion list for GROMACS users gmx-users@gromacs.org *已发送：* 2009/7/21(周二), 上午9:41:42 *主题：* Re: 回复： [gmx-users] Re: Some questions on Tabulated Dihedral Potential Ran Friedman wrote: Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX Correction: der =聽 (y[N+1] - y[N-1]) * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote: Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's 聽your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH ___ 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 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.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/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 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ 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] comparison of gromacs in CENTOS and UBUNTU
Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.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/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] PDB and GRO files
Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie ___ 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] PDB and GRO files
Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com wrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie ___ 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 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] PDB and GRO files
Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them?? Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br wrote: Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.comwrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie ___ 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 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 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] PDB and GRO files
Jamie Seyed wrote: Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? That's going to depend entirely upon what that system is. Building a protein or peptide is not so trivial. Building a small molecule is fairly straightforward using programs like PRODRG (online) or xLeap (part of AmberTools). That said, if your goal is to simulate some arbitrary small molecules, the previous advice of using pdb2gmx will not apply. You will have to build the topologies yourself. Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them?? If you cite some examples, maybe someone can point you in the right direction. The Gromacs webpage is currently migrating to a new site; old webpages can be accessed by appending old to the URL, i.e. http://oldwww.gromacs.org is the old home page. -Justin Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote: Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/ Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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] Re: comparison of gromacs in CENTOS and UBUNTU
Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Your question is senseless. The linux distribution will not affect gromacs performance. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] Re: PDB and GRO files
Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie Jamie, Please see the help for genbox, genconf and editconf utlities of the gromacs package. It seems you should be interested in Protein Data Bank as well: http://www.rcsb.org/pdb/home/home.do ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] PDB and GRO files
Hi Justin, On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? That's going to depend entirely upon what that system is. Building a protein or peptide is not so trivial. Building a small molecule is fairly straightforward using programs like PRODRG (online) or xLeap (part of AmberTools). That said, if your goal is to simulate some arbitrary small molecules, the previous advice of using pdb2gmx will not apply. You will have to build the topologies yourself. Is the result of using these programs a pdb file or gro.. would you please explain a little bit? The systems that I want to simulate are fullerene and CNT. But before that I will simulate a box of water, spce. In this case is it ok to use spc216.pdb (??) or I should use the programs you mentioned? Sorry for these simple questions.. Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them?? If you cite some examples, maybe someone can point you in the right direction. The Gromacs webpage is currently migrating to a new site; old webpages can be accessed by appending old to the URL, i.e. http://oldwww.gromacs.org is the old home page. For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you mentioned, but I can not open links on the page. All of them (check force field for example) can not open with like this message Site settings could not be loaded... Is it the page I should use to get a pdb file for my system?? I really appreciate if you let me know the exact web-address to use PRODRG or xLeap (?). Thanks a lot, Jamie -Justin Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote: Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/ Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] Re: PDB and GRO files
Is the result of using these programs a pdb file or gro.. would you please explain a little bit? The systems that I want to simulate are fullerene and CNT. But before that I will simulate a box of water, spce. In this case is it ok to use spc216.pdb For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you mentioned, but I can not open links on the page. All of them (check force field for example) can not open with like this message Site settings could not be loaded... Is it the page I should use to get a pdb file for my system?? I really appreciate if you let me know the exact web-address to use PRODRG or xLeap (?). 1. spc216.pdb should contain SPC water, not SPCE. 2. You can convert your coordinates to PDB format using almost any molecular viewer (like MOLEKEL, VMD, etc). 3. The nanotubes files (coordinates and topologies) as well as a number of already equilibrated systems were uploaded by me to the topology section of the old site. I guess they are still accessible. You may also want to look for Christopher Stiles' wonderful page with many details. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] PDB and GRO files
Jamie Seyed wrote: Hi Justin, On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? That's going to depend entirely upon what that system is. Building a protein or peptide is not so trivial. Building a small molecule is fairly straightforward using programs like PRODRG (online) or xLeap (part of AmberTools). That said, if your goal is to simulate some arbitrary small molecules, the previous advice of using pdb2gmx will not apply. You will have to build the topologies yourself. Is the result of using these programs a pdb file or gro.. would you please explain a little bit? The documentation of each program will explain the output formats. The systems that I want to simulate are fullerene and CNT. But before Then neither PRODRG nor xLeap will be of use to you; xLeap might work, but it's probably about the hardest way to do it :) that I will simulate a box of water, spce. In this case is it ok to use spc216.pdb (??) or I should use the programs you mentioned? Use spc216.gro - it's a pre-equilibrated box that is suitable for use in further simulations. Sorry for these simple questions.. Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them?? If you cite some examples, maybe someone can point you in the right direction. The Gromacs webpage is currently migrating to a new site; old webpages can be accessed by appending old to the URL, i.e. http://oldwww.gromacs.org http://oldwww.gromacs.org/ is the old home page. For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you mentioned, but I can not open links on the page. All of them (check force field for example) can not open with like this message Site settings could not be loaded... Use Google to search for PRODRG; the link in the wiki article is incorrect. But as I said above, for your purposes, PRODRG is not useful. Is it the page I should use to get a pdb file for my system?? I really appreciate if you let me know the exact web-address to use PRODRG or xLeap (?). Use Google to find things. This page is probably where you will want to start: http://www.gromacs.org/WIKI-import/Carbon_Nanotube -Justin Thanks a lot, Jamie -Justin Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote: Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically,after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/ http://laips.sel.eesc.usp.br/ Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks, Jamie
[gmx-users] reliability of NOTES
Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:38 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? As long as those vectors define the box size and not necessarily the system size (i.e., largest coordinate - smallest coordinate). You can do this with a .pdb file, I think on the CRYST line, if you prefer. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:08 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms
[gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU
Hi! In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is approximatedely twice slower than in a installation in an entire HD. If you need to install Linux in dual boot, maybe CentOS is a better choice. Best regards, Laércio Pol-Fachin --- Em ter, 21/7/09, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org escreveu: 1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal) Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST) From: jagannath mondal jmondal2...@yahoo.co.in Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU To: gmx-users@gromacs.org Message-ID: 410193.9922...@web7906.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.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/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] Re: comparison of gromacs in CENTOS and UBUNTU
I don't see how hard disk space of the OS has anything to do with the speed of Gromacs. Are the machines you refer to identical in terms of hardware (CPU, RAM, etc) as well as the compilers used to install the software? I have installed Gromacs under several different OS - Mac, Ubuntu Linux, Yellowdog Linux, and Fedora Linux. The only real speed difference comes from the hardware. -Justin Laercio Pol Fachin wrote: Hi! In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is approximatedely twice slower than in a installation in an entire HD. If you need to install Linux in dual boot, maybe CentOS is a better choice. Best regards, Laércio Pol-Fachin --- Em *ter, 21/7/09, gmx-users-requ...@gromacs.org /gmx-users-requ...@gromacs.org/* escreveu: 1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal) Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST) From: jagannath mondal jmondal2...@yahoo.co.in http://br.mc515.mail.yahoo.com/mc/compose?to=jmondal2...@yahoo.co.in Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU To: gmx-users@gromacs.org http://br.mc515.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org Message-ID: 410193.9922...@web7906.mail.in.yahoo.com http://br.mc515.mail.yahoo.com/mc/compose?to=410193.9922...@web7906.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/ - Celebridades http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/ - Música http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/ - Esportes http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/ ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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] Re: reliability of NOTES
Payman Pirzadeh wrote: Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Very reliable - the statistical ensemble from the Berendsen thermostat does not correspond to any known ensemble. This has been well-documented in the literature for years. T-coupling choices are listed in the manual: http://manual.gromacs.org/current/online/mdp_opt.html#tc Note that V-rescale is one of them :) Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? I can't recall having read anything about this in particular, but it's probably somewhere in the literature as well. Use the Parrinello-Rahman barostat instead. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:38 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? As long as those vectors define the box size and not necessarily the system size (i.e., largest coordinate - smallest coordinate). You can do this with a .pdb file, I think on the CRYST line, if you prefer. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:08 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate
[gmx-users] Re: reliability of NOTES
Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] PDB and GRO files
Yeah, we are friendly. :) Don't hesitate to ask if you experience future problems. ~ Vitaly On Wed, Jul 22, 2009 at 1:55 AM, Jamie Seyed jamie.se...@gmail.com wrote: Thank you for your help and comments. -Jamie ___ 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] Re: gmx-users Digest, Vol 63, Issue 110
In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is approximatedely twice slower than in a installation in an entire HD. If you need to install Linux in dual boot, maybe CentOS is a better choice. If one believes you, it comes out that non-running windows interfere gromacs run. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] How to get the rotational correlation time of the non-equilibrium simulation
Dear Users: I am wondering how I can get rotation correlation time of non-equilibrium simulation? is there any command letting me do that? Or I have to do it manually? My second question is : if Gromacs can calculate the standard error by using the blocking average method and how? Thanks for your help in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Re: comparison of gromacs in CENTOS and UBUNTU
Obviously the HD space has nothing to do with GMX performance (unless it is full, of course), but the use of Ubuntu precompiled packages can affect drastically the GMX performance, especially if you are also using pre-compiled MPI library package. An important rule when you are interested in High Performance Computing: Compile ALL your softwares (the last REALLY stable version) using GOOD compilers (GCC is fine, but if you have access to Intel or Portland ones is better). This rule is highly recommended ALSO to your linux kernel. Never leave the important and easy work of compile your important programs with unknown people! Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Quoting Justin A. Lemkul jalem...@vt.edu: I don't see how hard disk space of the OS has anything to do with the speed of Gromacs. Are the machines you refer to identical in terms of hardware (CPU, RAM, etc) as well as the compilers used to install the software? I have installed Gromacs under several different OS - Mac, Ubuntu Linux, Yellowdog Linux, and Fedora Linux. The only real speed difference comes from the hardware. -Justin Laercio Pol Fachin wrote: Hi! In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is approximatedely twice slower than in a installation in an entire HD. If you need to install Linux in dual boot, maybe CentOS is a better choice. Best regards, Laércio Pol-Fachin --- Em *ter, 21/7/09, gmx-users-requ...@gromacs.org /gmx-users-requ...@gromacs.org/* escreveu: 1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal) Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST) From: jagannath mondal jmondal2...@yahoo.co.in http://br.mc515.mail.yahoo.com/mc/compose?to=jmondal2...@yahoo.co.in Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU To: gmx-users@gromacs.org http://br.mc515.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org Message-ID: 410193.9922...@web7906.mail.in.yahoo.com http://br.mc515.mail.yahoo.com/mc/compose?to=410193.9922...@web7906.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi, I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor. Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/ - Celebridades http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/ - Música http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/ - Esportes http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/ ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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 WEBMAIL - IFSC - Instituto de FÃsica de São Carlos ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] PDB and GRO files
Hi Jamie. Another (free)options to generate the coordinate files (pdb or gro, they are basically the same and can be converted into another using the trjconv tool) are Molden and VMD. With Molden you can build a molecule from scratch easily. I recommend it to draw small molecules like drugs. VMD (version 1.8.7) has two tools that can be what you are looking for. With Molefacture plugin you can draw small molecules and peptides. With Nanotube Builder plugin you can easily build the CNTs you are interested. To construct fullerenes I don't konw any VMD plugin, but probably somebody has already done some plugin or script to generate this kind of molecules, try to search in google by fullerenes and VMD Cheers -- ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Quoting Jamie Seyed jamie.se...@gmail.com: Hi Justin, On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Hi, Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation? That's going to depend entirely upon what that system is. Building a protein or peptide is not so trivial. Building a small molecule is fairly straightforward using programs like PRODRG (online) or xLeap (part of AmberTools). That said, if your goal is to simulate some arbitrary small molecules, the previous advice of using pdb2gmx will not apply. You will have to build the topologies yourself. Is the result of using these programs a pdb file or gro.. would you please explain a little bit? The systems that I want to simulate are fullerene and CNT. But before that I will simulate a box of water, spce. In this case is it ok to use spc216.pdb (??) or I should use the programs you mentioned? Sorry for these simple questions.. Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them?? If you cite some examples, maybe someone can point you in the right direction. The Gromacs webpage is currently migrating to a new site; old webpages can be accessed by appending old to the URL, i.e. http://oldwww.gromacs.org is the old home page. For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you mentioned, but I can not open links on the page. All of them (check force field for example) can not open with like this message Site settings could not be loaded... Is it the page I should use to get a pdb file for my system?? I really appreciate if you let me know the exact web-address to use PRODRG or xLeap (?). Thanks a lot, Jamie -Justin Thanks for your help, Jamie On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli rodrigo_facci...@uol.com.br mailto:rodrigo_facci...@uol.com.br wrote: Hi, If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation. Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it. I hope that this email helped you. Cheers, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br http://laips.sel.eesc.usp.br/ Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed jamie.se...@gmail.com mailto:jamie.se...@gmail.com wrote: Hi, I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files? I appreciate your help for solve my basic problems. Thanks,
[gmx-users] genconf
OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Vitaly V. Chaban Sent: July 21, 2009 4:53 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] genconf
Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command “genconf”. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using “genconf” that I am missing? Doesn’t it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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] genconf
In my previous e-mail, I posted the amount of charge given by GROMACS: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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 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] genconf
Payman Pirzadeh wrote: In my previous e-mail, I posted the amount of charge given by GROMACS: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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] genconf
I am so sorry! I had sth in mind and I wrote sth else!!! My original box has zero charges and GROMACS shows no notes on this. As soon as the box is multiplies, then the note regarding the net charge shows up and causes the simulation to crash. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: In my previous e-mail, I posted the amount of charge given by GROMACS: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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] genconf
Payman Pirzadeh wrote: I am so sorry! I had sth in mind and I wrote sth else!!! My original box has zero charges and GROMACS shows no notes on this. As soon as the box is multiplies, then the note regarding the net charge shows up and causes the simulation to crash. Well, then, like I said, this is probably an accumulation of rounding errors. It can probably be ignored. The reason for the crash is more likely some kind of atomic overlap generated by the use of genconf. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: In my previous e-mail, I posted the amount of charge given by GROMACS: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing 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
RE: [gmx-users] genconf
Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option -dist help here? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: I am so sorry! I had sth in mind and I wrote sth else!!! My original box has zero charges and GROMACS shows no notes on this. As soon as the box is multiplies, then the note regarding the net charge shows up and causes the simulation to crash. Well, then, like I said, this is probably an accumulation of rounding errors. It can probably be ignored. The reason for the crash is more likely some kind of atomic overlap generated by the use of genconf. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: In my previous e-mail, I posted the amount of charge given by GROMACS: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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
Re: [gmx-users] genconf
Payman Pirzadeh wrote: Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option -dist help here? Maybe. I've never had to use it. I've replicated a few systems using genconf -nbox (water and lipids), but I've never encountered any problems. In theory, PBC should be maintained since all genconf is doing is translating your system by a certain factor according to box dimensions. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: I am so sorry! I had sth in mind and I wrote sth else!!! My original box has zero charges and GROMACS shows no notes on this. As soon as the box is multiplies, then the note regarding the net charge shows up and causes the simulation to crash. Well, then, like I said, this is probably an accumulation of rounding errors. It can probably be ignored. The reason for the crash is more likely some kind of atomic overlap generated by the use of genconf. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: In my previous e-mail, I posted the amount of charge given by GROMACS: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command genconf. My original box has non-zero charge, but the generated bigger box has some charges: Define non-zero. Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using genconf that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua mailto:cha...@univer.kharkov.ua,vvcha...@gmail.com mailto:vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] genconf
Payman Pirzadeh wrote: Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option -dist help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. 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
