[gmx-users] Finding centroid for a bunch of residues
Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for the particular site.. Is there any visualization tool that can do the same .. I mean Is there any molecular visualization tool that can help in finding out the ...centroid between a group of resuidues ? With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] steady
hi justin in during making mix solvent (30% for example) after making box I use trjconv -pbc .My pdb file lost the the arrange and it need long time for equilbrate and steady density.Is it right? or any suggestion about it? thanks -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] posres problem in 4.0_rc2. Bug in grompp?
Hi, My test posres systems work fine. Could you send me your input files and tpr file? Berk Date: Thu, 2 Oct 2008 17:20:07 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] posres problem in 4.0_rc2. Bug in grompp? Hi, I have a system in which I apply a posres on one atom. During em or md I get an error that I never had before: --- Program mdrun, VERSION 4.0_rc2 Source code file: mtop_util.c, line: 642 Software inconsistency error: Position restraint coordinates are missing --- Grompp runs withouth errors. When stargting mdrun, I get the error. The error is most likely in grompp: When running an older CVS-grompp (from last July), mdrun(4.0) works fine. When using the 4.0-grompp with the 4.0-mdrun, the error occurs. Or do I miss something? cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Preparing polystyrene
I am trying to use a .pdb for a polystyrene film (32 chains with 80 monomers each). The problem is that when I start running pdb2gmx I get the error that it can not find the residues (which are of course different from those in Gromacs). What would be the best thing to do? Have somebody a pdb or rtp file for Polystyrene? Which force filed would be more apropriate (united atoms)? Thank you. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: GMX 4.0 RC2: mdrun writes broken molecules?
I have encountered the same problem too. For water molecules not being broken in the mdrun, I think atoms in same charge group will not be divided into separate processors. It will be ok to use trjconv -pbc nojump/mol to get a clear visualization. Hi Justin, It's indeed the case that mdrun now writes broken molecules. Has to do with the domain decomposition and processors only keeping track of 'their' atoms. Too bad, but you'll just have to keep a .tpr around to make molecules whole again afterwards. Using trjconv -nojump with a suitable reference (not necessarily a .tpr) would also do it (and simultaneously remove the jumps...). Cheers, Tsjerk On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Hi, I've been running some simulations with Gromacs 4.0 RC2, and I've noticed something strange. In the output .gro file at the end of a run, the molecules in my system (a membrane protein) are broken, crossing periodic boundaries. This affects the lipids at the periphery of the box, in my case. Has there been some change since the previous version that mdrun is now writing broken molecules to fit everything within the unit cell? Or is this behavior unintentional? -Justin -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Finding centroid for a bunch of residues
Hi Everybody, adding a little to my question, can I view the co-ordinate of an atom by pointing at it using mouse or can I select an atom by specifying its co-ordinate only..? Does any of the tool in chimera, pymol, vmd is having such facility.? 2008/10/6 vivek sharma [EMAIL PROTECTED] Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for the particular site.. Is there any visualization tool that can do the same .. I mean Is there any molecular visualization tool that can help in finding out the ...centroid between a group of resuidues ? With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] some questions about gromacs
dcip1101 wrote: Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions carefully. 2. How to prepare parameters for a cofactor not included in the standard force fields? This is a very advanced topic. See here: http://wiki.gromacs.org/index.php/Parameterization 3. Any further suggestions to a new user to use the package better? Depends on what you are doing. Read lots of tutorials and consult the mailing list archive and wiki site (wiki.gromacs.org) if you have problems or are not certain how to implement certain features. -Justin Thanks so much for your time. Have a nice day. Jeffrey [广告] 特惠尝必胜客26道新品 http://popme.163.com/link/004584_0927_6221.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Finding centroid for a bunch of residues
Hi Vivek, adding a little to my question, can I view the co-ordinate of an atom by pointing at it using mouse or can I select an atom by specifying its co-ordinate only..? Does any of the tool in chimera, pymol, vmd is having such facility.? In VMD the coordinates of an atom you click on will be shwon in the console after pressing 0 (zero, not O :) while the OpenGL display is in focus (or selecting Query in the Mouse menu. You can select an atom by giving an appropriate selection under Graphics-Representations-Selected Atoms - like x = 1.0 and y = 1.0 and z = 1.0... Best, Michael -- http://www.defux.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] posres problem in 4.0_rc2. Bug in grompp?
Hi, There was a bug, but it would only show up when there was a moleculetype with only one position restraint and there was only one such molecule in the system. We were lucky that you have exactly such a system. I have fixed it in CVS for the next release. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] posres problem in 4.0_rc2. Bug in grompp? Date: Mon, 6 Oct 2008 08:57:03 +0200 Hi, My test posres systems work fine. Could you send me your input files and tpr file? Berk Date: Thu, 2 Oct 2008 17:20:07 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] posres problem in 4.0_rc2. Bug in grompp? Hi, I have a system in which I apply a posres on one atom. During em or md I get an error that I never had before: --- Program mdrun, VERSION 4.0_rc2 Source code file: mtop_util.c, line: 642 Software inconsistency error: Position restraint coordinates are missing --- Grompp runs withouth errors. When stargting mdrun, I get the error. The error is most likely in grompp: When running an older CVS-grompp (from last July), mdrun(4.0) works fine. When using the 4.0-grompp with the 4.0-mdrun, the error occurs. Or do I miss something? cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] some questions about gromacs
Hi, 1. Yes you can, please refer to this http://chemistry.csulb.edu/ffamber/ There is a script to convert amber formats into gromacs format. You can get it from here http://chemistry.csulb.edu/ffamber/tools.html It is only tested for small molecules although it should work for bigger system. 2. Normally you have to run geometry optimization using a QM package (Gaussian or Gamess; Gamess is free. Sometimes they can give different results, though) at B3LYP/6-31G* level (I think this level is enough for most cases). Then calculate ESP at level HF/6-31G* and derive the RESP charge using Antechamber if your molecule is simple. Finally, you need to judge and add in mixing parameters bases on similar structure. Gaff and Antechamber can do this step for you if your molecule is simple enough. That's for preparing parameters for your molecules in Amber force field. 3. Nothing other than reading lots and experiencing yourself :). Good luck!!! Cheers -Original Message- From: [EMAIL PROTECTED] on behalf of dcip1101 Sent: Mon 10/6/2008 5:52 PM To: gmx-users@gromacs.org Subject: [gmx-users] some questions about gromacs Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? 2. How to prepare parameters for a cofactor not included in the standard force fields? 3. Any further suggestions to a new user to use the package better? Thanks so much for your time. Have a nice day. Jeffrey winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull.pdo Columns
Message: 1 Date: Sun, 5 Oct 2008 09:51:23 -0400 From: VENKATESH HARIHARAN [EMAIL PROTECTED] Subject: [gmx-users] Pull.pdo Columns To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Hello, I understand this topic has been dealt with previously, and I have read all the relative material from the archives, but I am still having trouble deciphering what each column corresponds to in the pull.pdo file for an AFM pull, with one pull group and one reference group, and pulling in only the X direction. From what I've read, the columns are as follows: Time RefX RefY RefZ PullX PullY PullZ SpringX SpringY SpringZ the columns should be (in GORMACS 3.3.3) Time RefX RefY RefZ PullX SprX PullY SprY PullZ SprZ you can check this, the pulldir+RefX should be SprX and so on... ...for a total of 10 columns. The problem is that when I use the values of for the reference group and pull group at time zero to calculate end to end distance, they do not correspond to my starting pdb file after solvation. Any thoughts? __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081005/271401ab/attachment-0001.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] questions about using GROMACS
Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? 2. How to prepare parameters for a cofactor not included in the standard force fields? 3. Any further suggestions to a new user to use the package better? Thanks so much for your time. Have a nice day. Jeffrey -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 54, Issue 22 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] steady
shahrbanoo karbalaee wrote: hi justin in during making mix solvent (30% for example) after making box I use trjconv -pbc .My pdb file lost the the arrange and it need long time for equilbrate and steady density.Is it right? or any suggestion about it? What option are you giving trjconv -pbc (whole, nojump, etc.)? Why do you need this? If your goal is to create a mixed solvent, simply using normal periodic boundary conditions during the simulation should be all you need. Post-processing will likely give you a distorted unit cell. -Justin thanks -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Finding centroid for a bunch of residues
vivek sharma wrote: Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for the particular site.. Is there any visualization tool that can do the same .. I mean Is there any molecular visualization tool that can help in finding out the ...centroid between a group of resuidues ? You will likely have to write a script that will do this for you. It can be accomplished, for example, with VMD, although my own personal experience with such scripting is somewhat limited. See for example: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5963.html That may give you some ideas. -Justin With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Finding centroid for a bunch of residues
Hi
It's easy to find centroid of a bunch of residues in
VMD.
For example,you want to find centroid of residue 1 5
8.
First,you input atomselect top {resid 1 5 8} in
console of VMD,if atomselect0 appear,then input
measure center atomselect0 weight mass,coordinate of
centroid will display.
For the second question,in VMD,when you pointing at an
atom,its coordinate will display in console.
If you want select an atom by specifying its
coordinate,in Selected atoms text box,you can input
coordinate range of atoms,e.g. x3 and x4.
-- Lu Tian
Hi Everybody,
adding a little to my question, can I view the
co-ordinate of an atom by
pointing at it using mouse or can I select an atom
by specifying its
co-ordinate only..?
Does any of the tool in chimera, pymol, vmd is
having such facility.?
2008/10/6 vivek sharma [EMAIL PROTECTED]
Hi there,
This is the question out of gromacs..but I need it
urgently.. and I hope
this is the only place where I can get such expert
to solve my query...
while trying to restrict my MDRUN for a particular
site of the protein
molecule I want to visualize the site and find out
the centroid for the
particular site..
Is there any visualization tool that can do the
same ..
I mean Is there any molecular visualization tool
that can help in finding
out the ...centroid between a group of resuidues ?
With Thanks,
Vivek
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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Re: [gmx-users] Re: Finding centroid for a bunch of residues
Thanks a lot everybody for the replies...
it has really saved a lot of time for me...:)
With Thanks,
Vivek
2008/10/6 sobereva [EMAIL PROTECTED]
Hi
It's easy to find centroid of a bunch of residues in
VMD.
For example,you want to find centroid of residue 1 5
8.
First,you input atomselect top {resid 1 5 8} in
console of VMD,if atomselect0 appear,then input
measure center atomselect0 weight mass,coordinate of
centroid will display.
For the second question,in VMD,when you pointing at an
atom,its coordinate will display in console.
If you want select an atom by specifying its
coordinate,in Selected atoms text box,you can input
coordinate range of atoms,e.g. x3 and x4.
-- Lu Tian
Hi Everybody,
adding a little to my question, can I view the
co-ordinate of an atom by
pointing at it using mouse or can I select an atom
by specifying its
co-ordinate only..?
Does any of the tool in chimera, pymol, vmd is
having such facility.?
2008/10/6 vivek sharma [EMAIL PROTECTED]
Hi there,
This is the question out of gromacs..but I need it
urgently.. and I hope
this is the only place where I can get such expert
to solve my query...
while trying to restrict my MDRUN for a particular
site of the protein
molecule I want to visualize the site and find out
the centroid for the
particular site..
Is there any visualization tool that can do the
same ..
I mean Is there any molecular visualization tool
that can help in finding
out the ...centroid between a group of resuidues ?
With Thanks,
Vivek
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Finding centroid for a bunch of residues
Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for the particular site.. Is there any visualization tool that can do the same .. I mean Is there any molecular visualization tool that can help in finding out the ...centroid between a group of resuidues ? Pymol has a script that computes the center of mass for a selection, and optionally, moves this center of mass to the origin: http://pymolwiki.org/index.php/COM Haven't used it myself, so I can't vouch for its effectiveness. Steve Kirk -- Dr. Steven R. Kirk [EMAIL PROTECTED], [EMAIL PROTECTED] Dept. of Technology, Mathematics Computer Science (P)+46 520 223215 University West (F)+46 520 223299 Trollhattan 461 86 SWEDEN http://beacon.webhop.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:gmx-users Digest, Vol 54, Issue 23
Hi Justin, Thanks so much for your prompt response. If using AMBER force field, can one construct the parameters of non-standard molecules through ANTECHAMBER in AMBER package? Thanks in advance. Have a nice day. --- Jeffrey Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul Subject: Re: [gmx-users] some questions about gromacs To: Discussion list for GROMACS users Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed dcip1101 wrote: Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions carefully. 2. How to prepare parameters for a cofactor not included in the standard force fields? This is a very advanced topic. See here: http://wiki.gromacs.org/index.php/Parameterization 3. Any further suggestions to a new user to use the package better? Depends on what you are doing. Read lots of tutorials and consult the mailing list archive and wiki site (wiki.gromacs.org) if you have problems or are not certain how to implement certain features. -Justin Thanks so much for your time. Have a nice day. Jeffrey [EMAIL PROTECTED] 写道： Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. some questions about gromacs (dcip1101) 2. RE: Heat Flux and Lambda (Berk Hess) 3. Re: some questions about gromacs (Justin A. Lemkul) 4. Re: Pull.pdo Columns (Thomas Schlesier) 5. Re: steady (Justin A. Lemkul) 6. questions about using GROMACS (dcip1101) -- Message: 1 Date: Mon, 6 Oct 2008 17:52:45 +0800 (CST) From: dcip1101 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081006/6a76ccd9/attachment-0001.html -- Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 4 Date: Mon, 6 Oct 2008 13
Re: [gmx-users] Re:gmx-users Digest, Vol 54, Issue 23
dcip1101 wrote: Hi Justin, Thanks so much for your prompt response. If using AMBER force field, can one construct the parameters of non-standard molecules through ANTECHAMBER in AMBER package? Yes. The parameter files can then be converted to Gromacs format using scripts present in the User Contributions section of the Gromacs website. -Justin Thanks in advance. Have a nice day. --- Jeffrey Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul Subject: Re: [gmx-users] some questions about gromacs To: Discussion list for GROMACS users Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed dcip1101 wrote: Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions carefully. 2. How to prepare parameters for a cofactor not included in the standard force fields? This is a very advanced topic. See here: http://wiki.gromacs.org/index.php/Parameterization 3. Any further suggestions to a new user to use the package better? Depends on what you are doing. Read lots of tutorials and consult the mailing list archive and wiki site (wiki.gromacs.org) if you have problems or are not certain how to implement certain features. -Justin Thanks so much for your time. Have a nice day. Jeffrey [EMAIL PROTECTED] 写道： Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. some questions about gromacs (dcip1101) 2. RE: Heat Flux and Lambda (Berk Hess) 3. Re: some questions about gromacs (Justin A. Lemkul) 4. Re: Pull.pdo Columns (Thomas Schlesier) 5. Re: steady (Justin A. Lemkul) 6. questions about using GROMACS (dcip1101) -- Message: 1 Date: Mon, 6 Oct 2008 17:52:45 +0800 (CST) From: dcip1101 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081006/6a76ccd9/attachment-0001.html -- Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu
[gmx-users] problem running gromacs job
Dear Sirs, We are trying to use Gromacs software at a academic and research centre in Madrid, Spain. For this purpose, we downloaded gromacs-3.3.3.tar.gz from your webpage and compiled it as follows: CC=/opt/intel/cce/10.0.023/bin/icc CFLAGS=-O2 -L/opt/intel/mkl/9.1/lib/em64t -I/opt/intel/mkl/9.1/include MPILIBS=-L/opt/mpich-ch_p4-icc-large-1.2.7/lib/ ./configure --with-fft=mkl --enable-mpi --enable-double --disable-threads --prefix=/opt/gromacs-3.3.3 --disable-nice Bellow you can find the way we submitted the job an the error we obtained. In order to dismiss a MPI problem we have also used MPICH and LAM. I look forward to your help with this problem. Yours faithfully, Sonia Martinez Dra. Sonia Martínez Hedo Química Computacional ALTRAN / CTI-CSIC [EMAIL PROTECTED] gromacs]$ /opt/mpich-ch_p4-icc-large-1.2.7/bin/mpirun -machinefile machines -np 2 /opt/gromacs-3.3.3/bin/mdrun_d -np 2 -s 1HYG-pt.tpr -o 1HYG-pt.trr -c 1HYG-pt.gro -e 1HYG-pt.edr -x 1HYG-pt.xtc -v NNODES=2, MYRANK=0, HOSTNAME=trueno34.csic.es NNODES=2, MYRANK=1, HOSTNAME=trueno34.csic.es NODEID=0 argc=14 :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /opt/gromacs-3.3.3/bin/mdrun_d (double precision) (-: Option Filename Type Description -s1HYG-pt.tpr InputGeneric run input: tpr tpb tpa xml -o1HYG-pt.trr Output Full precision trajectory: trr trj -x1HYG-pt.xtc Output, Opt! Compressed trajectory (portable xdr format) -c1HYG-pt.gro Output Generic structure: gro g96 pdb xml -e1HYG-pt.edr Output Generic energy: edr ene -g md.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -fieldfield.xvg Output, Opt. xvgr/xmgr file -tabletable.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -rerunrerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpitpi.xvg Output, Opt. xvgr/xmgr file -eisam.edi Input, Opt. ED sampling input -eosam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jobam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -pi pull.ppa Input, Opt. Pull parameters -popullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint19 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int2 Number of nodes, must be the same as used for grompp
[gmx-users] how long it take to run do_dssp
Dear gmxuser I want to analyze the secondary structure of a protein after a 10ns simulation run but I do not know how long it will take because I run it for more than 2 hours but it is still running.I don't know whether I am encountering any problem , in the manual it is mentioned that the program is very slow. But it is not mention how long. I saw in gmx mailing list that somebody has my problem before but his problem solved by my_dssp. Unfortunately, I could not also run my_dssp and I faced with many error. tnx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how long it take to run do_dssp
On Mon, 6 Oct 2008 17:27:31 +0200 (CEST) Morteza Khabiri [EMAIL PROTECTED] wrote: Dear gmxuser I want to analyze the secondary structure of a protein after a 10ns simulation run but I do not know how long it will take because I run it for more than 2 hours but it is still running.I don't know whether I am encountering any problem , in the manual it is mentioned that the program is very slow. But it is not mention how long. I saw in gmx mailing list that somebody has my problem before but his problem solved by my_dssp. Unfortunately, I could not also run my_dssp and I faced with many error. Do it first on one conformation, then 10 from the trajectory (-b -e options) and you can get an estimate. tnx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - NMR and Computation University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Citing the most recent version of GROMACS
Hi, gromacs-4.0.pdf makes it look like the correct citation is van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., Berendsen, H. J. C. (2005) GROMACS: Fast, Flexible and Free. J. Comp. Chem. 26, 1701-1718. The README in the current tarball lists * GROMACS: A message-passing parallel molecular dynamics implementation H.J.C. Berendsen, D. van der Spoel and R. van Drunen Comp. Phys. Comm. 91, 43-56 (1995) * GROMACS 3.0: A package for molecular simulation and trajectory analysis Erik Lindahl, Berk Hess and David van der Spoel J. Mol. Mod. 7, 306-317 (2001) I'm wondering, however, if I should cite Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E. (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, J. Chem. Theory Comput., 4, 435-447. Which one is preferred if I just want to say GROMACS (ref)? (Apologies in advance: I searched the list archives and looked around on the website, but didn't see the answer in an obvious place.) Thanks, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) http://www.umich.edu/~mlerner ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a question about template.c
Hello, When I used template.c to make my own tool, I always got the progress information like Reading frame 60 time 60.000 after the Gromacs copyright information. Sometimes I want to run my tool in background. But these reading frame messages still jump out even after I use the command. Because I may need to do other things in the same terminal, these messages are annoying. I'm wondering if there is a simple way to redirect these outputs. Thanks very much. Lanyuan Lu _ 新年换新颜，快来妆扮自己的MSN给心仪的TA一个惊喜！ http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] a question about template.c
LuLanyuan a écrit : Hello, When I used template.c to make my own tool, I always got the progress information like Reading frame 60 time 60.000 after the Gromacs copyright information. Sometimes I want to run my tool in background. But these reading frame messages still jump out even after I use the command. Because I may need to do other things in the same terminal, these messages are annoying. I'm wondering if there is a simple way to redirect these outputs. Thanks very much. Lanyuan Lu command command.out or nohup command depending what you want to do cheers _ 新年换新颜，快来妆扮自己的MSN给心仪的TA一个惊喜！ http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:Research Assistant tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] a question about template.c
* Nicolas [EMAIL PROTECTED] [2008-10-06 17:22:44 -0600]: LuLanyuan a écrit : Hello, When I used template.c to make my own tool, I always got the progress information like Reading frame 60 time 60.000 after the Gromacs copyright information. Sometimes I want to run my tool in background. But these reading frame messages still jump out even after I use the command. Because I may need to do other things in the same terminal, these messages are annoying. I'm wondering if there is a simple way to redirect these outputs. Thanks very much. Lanyuan Lu command command.out or nohup command depending what you want to do cheers And to provide a small explanation, you see this line, because it is written to the stderr. If you use just '' only the stdout is written to the file. '' bundles both the stderr and stdout to one single file. /Flo _ ??MSNTA?? http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Computational and Theoretical Softmatter Biophysics group Frankfurt Institute for Advanced Studies Johann-Wolfgang-Goethe University Ruth-Moufang-Str. 1 60438 Frankfurt am Main Phone: +49(0)69 / 798 - 47522 Fax: +49(0)69 / 798 - 47611 EMail: [EMAIL PROTECTED] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert pgpJmI8MxaRk1.pgp Description: PGP signature ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] a question about template.c
Sorry, I didn't say it clearly. I used command command.out and it didn't work. I just tried nohup thing and it's the same. It seems to me the redirect doesn't work for the reading frame messages. Lanyuan Date: Mon, 6 Oct 2008 17:22:44 -0600 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] a question about template.c LuLanyuan a écrit : Hello, When I used template.c to make my own tool, I always got the progress information like Reading frame 60 time 60.000 after the Gromacs copyright information. Sometimes I want to run my tool in background. But these reading frame messages still jump out even after I use the command. Because I may need to do other things in the same terminal, these messages are annoying. I'm wondering if there is a simple way to redirect these outputs. Thanks very much. Lanyuan Lu command command.out or nohup command depending what you want to do cheers _ 新年换新颜，快来妆扮自己的MSN给心仪的TA一个惊喜！ http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！ http://get.live.cn/product/photo.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] setting constraints to incomplete protein structures
Hello, My responses are as follows: My questions: 1) Is it a good idea to use such catalytic domain structures for MD simulation? Or should I only use complete protein structures for MD? That depends entirely upon what you are interested in simulating. I am interested in predicting the binding energy (via further processing using a docking software) of a ligand to a specific protein target based on the conformation of the binding pocket after MD. How will missing residues in the other parts of the protein target affect the MD run for such purposes? 2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to constraint any atoms at the 'edges' during the MD run? What kind of edges? Those that are adjacent to the missing segments? If that's what you mean, see distance *restraints* or position *restraints*. Yes, I meant atoms that are adjacent to the missing segments. When should I use distance restraints and when should I use position restraints? I have a new question: What if the protein-ligand complex structure obtained from PDB contains chloride ions? How should I handle any ions during the MD runs? Restraint them as well? Or should I just let them go through MD without any restraints? regards, wk yeo _ Manage multiple email accounts with Windows Live Mail effortlessly. http://www.get.live.com/wl/all ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] setting constraints to incomplete protein structures
wk yeo wrote: Hello, My responses are as follows: My questions: 1) Is it a good idea to use such catalytic domain structures for MD simulation? Or should I only use complete protein structures for MD? That depends entirely upon what you are interested in simulating. I am interested in predicting the binding energy (via further processing using a docking software) of a ligand to a specific protein target based on the conformation of the binding pocket after MD. How will missing residues in the other parts of the protein target affect the MD run for such purposes? In biology, structure leads to function. Missing residues may lead to spurious behavior, such as destabilization of the protein structure. 2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to constraint any atoms at the 'edges' during the MD run? What kind of edges? Those that are adjacent to the missing segments? If that's what you mean, see distance *restraints* or position *restraints*. Yes, I meant atoms that are adjacent to the missing segments. When should I use distance restraints and when should I use position restraints? Distance restraints are what you are probably looking for. You can fix the distance between the backbone atoms to the distance found in the crystal structure. As for whether or not you can be confident in doing so is up to you. Position restraints are typically applied during solvent equilibration to allow the solvent to orient around the solute. I have a new question: What if the protein-ligand complex structure obtained from PDB contains chloride ions? How should I handle any ions during the MD runs? Restraint them as well? Or should I just let them go through MD without any restraints? If the ions were part of the precipitant or some sort of stabilizing co-solvent, they may be unnatural and therefore safe to ignore. Adding (at least) counterions to an MD simulation is routine, so you may end up adding those ions back within during solvation. -Justin regards, wk yeo _ Manage multiple email accounts with Windows Live Mail effortlessly. http://www.get.live.com/wl/all -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] one question about g_rdf under version 3.3.3
Hi, all, I have one question about g_rdf under version 3.3.3: g_rdf has two options:-com and -rdf. According to g_rdf -h, -com calculates the center of mass of the first group, -rdf calculate the rdf type: atom, molecule-COM/COG, residue-COM/COG. My question is -rdf calculates the atom/com/cog of the first(reference) group? OR the second group? 1. if -rdf calculates the fist group, -com should not be used with atom/mol_cog/res_cog. However, a test combing -com and -rdf atom gives a rdf curve! 2. if -rdf calculate the second group, g_rdf -h is kind of unclear, I think! Any suggestion is welcome! regards, Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Citing the most recent version of GROMACS
Michael Lerner wrote: Hi, gromacs-4.0.pdf makes it look like the correct citation is van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., Berendsen, H. J. C. (2005) GROMACS: Fast, Flexible and Free. J. Comp. Chem. 26, 1701-1718. The README in the current tarball lists * GROMACS: A message-passing parallel molecular dynamics implementation H.J.C. Berendsen, D. van der Spoel and R. van Drunen Comp. Phys. Comm. 91, 43-56 (1995) * GROMACS 3.0: A package for molecular simulation and trajectory analysis Erik Lindahl, Berk Hess and David van der Spoel J. Mol. Mod. 7, 306-317 (2001) I'm wondering, however, if I should cite Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E. (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, J. Chem. Theory Comput., 4, 435-447. Which one is preferred if I just want to say GROMACS (ref)? (Apologies in advance: I searched the list archives and looked around on the website, but didn't see the answer in an obvious place.) Thanks, -Michael If you used the most recent CVS version, the proper citation is Hess 2008. We'll update the manual etc. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] steady
Dear justin you are right .that file was distorted.I used -pbc without no jump.I need to use trjconv for minimized the box .please advise me. -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
