Re: [gmx-users] help---How to define new residue in GROMACS?
?? wrote: My problem is How to define new residue in GROMACS? i have made a 3-d structure model for a protein based on a template protein??which has a heme group. befor runing the gromacs molecular simulation,i must define the heme group as a new residue,How to define new residue in GROMACS? You need both suitable parameters for your desired forcefield, and then to construct a correct topology. The required formats are described in chapter 5 of the manual. You would be well advised to get some experience in how the work-flow operates by running normal simulations on simple proteins, e.g. in tutorials. If you wish to use pdb2gmx to create the topology, you will need to modify the residue topology file (.rtp) to add the new residue. http://oldwiki.gromacs.org/index.php/specbond.dat may also need to be changed to link the heme group properly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_wham problem
Oh, that would be convenient. Thanks. --- 09年8月3日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] g_wham problem 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年8月3日,周一,上午9:01 accomp lin wrote: Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is accomp...@student.dlut.edu.cn mailto:accomp...@student.dlut.edu.cn The Gromacs 4.0.x series contains a fixed g_wham that can handle the .pdo output of Gromacs 3.3.x. Using this official version might make it easier to get technical support, should you need it. -Justin Thanks a lot Jiaqi 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 list 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. 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 list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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
[gmx-users] Fwd: help-how to define a new residue in gromacs ?
This is what the GMX user list is for. Please post such requests there. Tsjerk -- Forwarded message -- From: 郭建路 zimoguojia...@163.com Date: 2009/8/4 Subject: help-how to define a new residue in gromacs ? To: tsjerkw tsje...@gmail.com HI Tsjerk: can you help me ? My problem is How to define new residue in GROMACS? i have made a 3-d structure model for a protein based on a template protein，which has a heme group. befor runing the gromacs molecular simulation,i must define the heme group as a new residue,How to define new residue in GROMACS? thanks ! yours guojianlu 没有广告的终身免费邮箱,www.yeah.net -- 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://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] query about simulation of a protein containg a metal ion
Dear Sir, I want to simulate a protein with a CA2+ ion and one crystal water using G431 force field, simulation of the protein without the metal ion went off successfully,But while running the simulation with the metal ion it's giving a fatal error during position restrained molecular dynamics, Fatal error: Group CA2+ not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Upto energy minimisation I have modified aminoacids.dat and other required files, it's not giving any error messege. During PR dynamics it's giving an error messege --- Program grompp, VERSION 4.0.5 Source code file: readir.c, line: 1075 Fatal error: 1 atoms are not part of any of the T-Coupling groups --- If I incorporate CA2+ ion in the mdp file it's giving Fatal error: Group CA2+ not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. if I use -n option it's giving --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- I don't understand what else files should be considered and manually edited..Please help.While running pdb2gmx CA2+ ion is considered as follows. type resnr residue CA2+ CA CA Please suggest what should be taken into account while running the simulation with the metal ion. regards Sangeeta Kundu See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.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] reg mopac gromacs installation
dear Mark Abraham sir, pardon for the disturbence through mail thank you for your atonce reply herafter i will contact u throug the gmx mailing list. please sorry for the inconvience. i am in budding stage in gromacs MD research --- On Tue, 4/8/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] reg mopac gromacs installation To: Gromacs Users gmx-users@gromacs.org Date: Tuesday, 4 August, 2009, 5:10 AM vidhya sankar wrote: i think it either needs fortran or c compiler am i correct . please mail me Please leave GROMACS correspondence on the mailing list. Yes, you will need either a FORTRAN or C compiler. Please read the documentation to find out. I don't know which, and don't care to find out :-) Mark --- On Mon, 3/8/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] reg mopac gromacs installation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 3 August, 2009, 5:15 AM vidhya sankar wrote: dear gmx user , i am doing QM/MM using MOPAC/GROMACS when i configure mopac7-1.10 the software using for the interface with gromacs by ../configure command i got error as follows configure error: f2c or g2c library cannot be found . solution for the above error would be appericiated reply please thanks in advance Solution: install f2c or g2c. Google is your friend. Probably the installation documentation for this port of GROMACS should talk about this issue. Mark ___ gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com ___ gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 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
RE: [gmx-users] FudgeLJ
No, you can not use pair parameter generation at all with Buckingham, since 1-4 interactions are always LJ and you can not convert Buckingham to LJ parameters. Unfortunately Gromacs 4.0 does not check for gen-pairs=yes, Gromacs 4.1 will give a fatal error when you turn it on. Dispersion correction works for Buckingham. Berk To: gmx-users@gromacs.org From: apal...@nd.edu Date: Mon, 3 Aug 2009 20:22:52 -0400 Subject: [gmx-users] FudgeLJ To whom this may concern, Is it possible to use FudgeLJ to scale 1-4 interactions when using a Buckingham Potential? Also, are long range corrections implemented for the Buckingham Potential? Thank you, Andrew _ 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://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] g_vanhove output
Hi all, I believe there is a mistake in g_vanhove in version 4.0.5 The 'xvg' output file labels the y axis as G, with nm^-1 as units. From the units, I guessed that the output was actually r^2 G, however the initial slope is linear and not quadratic. After a few tries I concluded that the output is actually r*G, which is not something really useful. I wonder if someone could look at the code and confirm this doubt in one way or another. Many thank, Marcelo Carignano. PS: I couldn't find this on the list, but it has been difficult to access the archives lately. ___ 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] g_vanhove output
Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference in interpretation comes from if you consider normalization of the volume of sphere-shells or not? Berk From: c...@purdue.edu To: gmx-users@gromacs.org Date: Tue, 4 Aug 2009 10:25:33 -0400 Subject: [gmx-users] g_vanhove output Hi all, I believe there is a mistake in g_vanhove in version 4.0.5 The 'xvg' output file labels the y axis as G, with nm^-1 as units. From the units, I guessed that the output was actually r^2 G, however the initial slope is linear and not quadratic. After a few tries I concluded that the output is actually r*G, which is not something really useful. I wonder if someone could look at the code and confirm this doubt in one way or another. Many thank, Marcelo Carignano. PS: I couldn't find this on the list, but it has been difficult to access the archives lately. ___ 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 _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ 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] g_vanhove output
Thanks Berk. I did look at the code, but it is not that easy to understand. My conclusion comes from this: for a diffusive regime, G(r) should be a gaussian function, with the diffusion coefficient characterizing the width. I did some tests, and I could match both curves (one from g_vanhove and the other from the diff.coef) only if I multiply the output of g_vanhove by r and normalizing again, which makes little sense to me. It would be ok to output G(r) or r^2*G(r), but to output r*G(r) seems a mistake Thanks again, Marcelo PS: I did consider the spherical integration. On Aug 4, 2009, at 10:41 AM, Berk Hess wrote: Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference in interpretation comes from if you consider normalization of the volume of sphere-shells or not? Berk From: c...@purdue.edu To: gmx-users@gromacs.org Date: Tue, 4 Aug 2009 10:25:33 -0400 Subject: [gmx-users] g_vanhove output Hi all, I believe there is a mistake in g_vanhove in version 4.0.5 The 'xvg' output file labels the y axis as G, with nm^-1 as units. From the units, I guessed that the output was actually r^2 G, however the initial slope is linear and not quadratic. After a few tries I concluded that the output is actually r*G, which is not something really useful. I wonder if someone could look at the code and confirm this doubt in one way or another. Many thank, Marcelo Carignano. PS: I couldn't find this on the list, but it has been difficult to access the archives lately. ___ gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php See all the ways you can stay connected to friends and family ___ 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] query about simulation of a protein containg a metal ion
sangeeta kundu wrote: a) Temperature coupling groups must include all atoms in the system. Do not couple handfuls of atoms separately. So Protein and Non-Protein are often right. b) If you use -n you need to supply an index file, which you might make with make_ndx. That index file must define all groups referred to above. These groups need not correspond to molecules, residues or anything else, so anything pdb2gmx said is not strictly relevant. Mark Dear Sir, I want to simulate a protein with a CA2+ ion and one crystal water using G431 force field, simulation of the protein without the metal ion went off successfully,But while running the simulation with the metal ion it's giving a fatal error during position restrained molecular dynamics, Fatal error: Group CA2+ not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Upto energy minimisation I have modified aminoacids.dat and other required files, it's not giving any error messege. During PR dynamics it's giving an error messege --- Program grompp, VERSION 4.0.5 Source code file: readir.c, line: 1075 Fatal error: 1 atoms are not part of any of the T-Coupling groups --- If I incorporate CA2+ ion in the mdp file it's giving Fatal error: Group CA2+ not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. if I use -n option it's giving --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- I don't understand what else files should be considered and manually edited..Please help.While running pdb2gmx CA2+ ion is considered as follows. typeresnr residue CA2+ CACA Please suggest what should be taken into account while running the simulation with the metal ion. regards Sangeeta Kundu See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.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 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] 1-4 interaction at distance larger than 1
Thank you very much, yes normally, the header of pdb file has remark 465 and 470. I just used the modeller loop to add the missing residues according to remark 470, and did not add following remark 465, is it right? because there are only RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER, it does not have atoms. By the way, there is a limit for modeller loop, if I want to addd more resiudes, are there any others softwares which are recommended. Thank you very much Yi On 03/08/2009 17:12, Justin A. Lemkul jalem...@vt.edu wrote: Yi Hou wrote: Dear Justin Thank you very much My commands are: 1. add hydrogens, get top and gro files pdb2gmx -f 1z92.pdb -o 1z92.gro -p 1z92.top If I'm not mistaken, 1z92 has substantial stretches of missing residues, and you probably had to model them in. I'd look at those regions as being potentially problematic. 2. specify the box size, and add water to the system editconf -f 1z92.gro -bt cubic -d 0.7 -o box.gro genbox -cp box.gro -cs spc216.gro -p 1z92.top -o sol.gro 3. grommpp -f em.mdp -p 1z92.top -c sol.gro -o em.tpr then found the system is charge -3 4. add 3NA+ ions in the SOL system genion -s em.tpr -p 1z92.tpr -p 1z92.top -o sol_ion.gro -pname NA+ -np 3 -nname CL- -nn 0 -random 5. perform the energy minimization simulation grompp -f em.mdp -p 1z92.top -o sol_ion.gro -o em.tpr mdrun -deffnm em -v Those commands until now then I should do position constraints and equil simulations with my pr.mdp and md.mdp parameters. I will check my .log file again to see if any errors occur I'd stop and diagnose why the minimization failed. If you can't finish EM, there is no point in running any sort of dynamics, equilibration or otherwise. -Justin Thank you very much Yi On 03/08/2009 15:56, Justin A. Lemkul jalem...@vt.edu wrote: houyi wrote: Dear all, I guess others have the same problem for me as well, and it may repeat to ask it again due to i am new for gromacs- 3.3.3. my protein is 1z92.pdb. when i perform the energy minimization , i got this error. but when i used for another small protein, which is 1ycr.pdb, it worked well for all. i choose the OPLS-AA/L all-atom force field my em.mdp is title = protein cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 i found the website and some one said change the table extension to 2 or 3 or maybe more, it works for this step, but after performing the postion constrains, it got the wrong results. so i guess i will not change the table extension, and i do not why it only work for small protein not for larger one, and i repeated sevel times, such as changing timesteps and rlist and rcoulomb and rvdw to 0.9. still not working. could anyone help me to explain this. Your system is blowing up due to some non-physical interaction. Tweaking the table-extension is probably not going to help. Some general references: http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-o ff http://oldwiki.gromacs.org/index.php/blowing_up Without knowing more about how you prepared the system (exact commands), then you will not likely get much more useful advice. Take a look at where things are falling apart (atom numbers printed in the .log file) and see if you can deduce the source of the problem. -Justin thank you very much Reards, Yi 您可以借助 Windows Live 整理、编辑和 共享您的照片。 http://www.microsoft.com/china/windows/windowslive/products/photo-gallery- ed it.aspx ___ 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 list
Re: [gmx-users] 1-4 interaction at distance larger than 1
Yi Hou wrote: Thank you very much, yes normally, the header of pdb file has remark 465 and 470. I just used the modeller loop to add the missing residues according to remark 470, and did not add following remark 465, is it right? because Normally one has to deal with *both* missing residues and missing atoms. Ignoring parts of this section can generate frustrations in trying to set up the system, or worse, incorrect answers, depending on the nature of what's missing. there are only RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER, it does not have atoms. By the way, there is a limit for modeller loop, if I want to addd more resiudes, are there any others softwares which are recommended. I haven't used Modeller much, but there certainly are programs out there. Loopy comes to mind, but I haven't done much loop building lately. Probably a simple Google search and look through relevant homology modeling and other simulation literature will turn up some useful programs. -Justin Thank you very much Yi On 03/08/2009 17:12, Justin A. Lemkul jalem...@vt.edu wrote: Yi Hou wrote: Dear Justin Thank you very much My commands are: 1. add hydrogens, get top and gro files pdb2gmx -f 1z92.pdb -o 1z92.gro -p 1z92.top If I'm not mistaken, 1z92 has substantial stretches of missing residues, and you probably had to model them in. I'd look at those regions as being potentially problematic. 2. specify the box size, and add water to the system editconf -f 1z92.gro -bt cubic -d 0.7 -o box.gro genbox -cp box.gro -cs spc216.gro -p 1z92.top -o sol.gro 3. grommpp -f em.mdp -p 1z92.top -c sol.gro -o em.tpr then found the system is charge -3 4. add 3NA+ ions in the SOL system genion -s em.tpr -p 1z92.tpr -p 1z92.top -o sol_ion.gro -pname NA+ -np 3 -nname CL- -nn 0 -random 5. perform the energy minimization simulation grompp -f em.mdp -p 1z92.top -o sol_ion.gro -o em.tpr mdrun -deffnm em -v Those commands until now then I should do position constraints and equil simulations with my pr.mdp and md.mdp parameters. I will check my .log file again to see if any errors occur I'd stop and diagnose why the minimization failed. If you can't finish EM, there is no point in running any sort of dynamics, equilibration or otherwise. -Justin Thank you very much Yi On 03/08/2009 15:56, Justin A. Lemkul jalem...@vt.edu wrote: houyi wrote: Dear all, I guess others have the same problem for me as well, and it may repeat to ask it again due to i am new for gromacs- 3.3.3. my protein is 1z92.pdb. when i perform the energy minimization , i got this error. but when i used for another small protein, which is 1ycr.pdb, it worked well for all. i choose the OPLS-AA/L all-atom force field my em.mdp is title = protein cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 i found the website and some one said change the table extension to 2 or 3 or maybe more, it works for this step, but after performing the postion constrains, it got the wrong results. so i guess i will not change the table extension, and i do not why it only work for small protein not for larger one, and i repeated sevel times, such as changing timesteps and rlist and rcoulomb and rvdw to 0.9. still not working. could anyone help me to explain this. Your system is blowing up due to some non-physical interaction. Tweaking the table-extension is probably not going to help. Some general references: http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-o ff http://oldwiki.gromacs.org/index.php/blowing_up Without knowing more about how you prepared the system (exact commands), then you will not likely get much more useful advice. Take a look at where things are falling apart (atom numbers printed in the .log file) and see if you can deduce the source of the problem. -Justin thank you very much Reards, Yi 您可以借助 Windows Live 整理、编辑和 共享您的照片。 http://www.microsoft.com/china/windows/windowslive/products/photo-gallery- ed it.aspx ___ 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
[gmx-users] Different force field: Gromacs vs Autodock
Hi I use Gromacs (ffG45a3) to run MD in the protein vs ligand system. Then, I use Autodock to calculate the protein-ligand binding energy. As I know the force fields are different between ffG45a3 and Autodock. The two different force fields explain the same system. How can I explain this? Thank you Lin ___ 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] g_vanhove output
I think I coded this all correctly, but the last time I used it was years ago. In 3D you could plot G(x), G1(y) and G(z), which are equal for an isotropic liquid. -or plots g(r) which is 2 pi r^2 G(r) Berk From: c...@purdue.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_vanhove output Date: Tue, 4 Aug 2009 11:02:51 -0400 Thanks Berk.I did look at the code, but it is not that easy to understand.My conclusion comes from this:for a diffusive regime, G(r) should be a gaussian function, with the diffusioncoefficient characterizing the width.I did some tests, and I could match both curves (one from g_vanhove and the other from the diff.coef) only if I multiply the output of g_vanhove by r and normalizing again, which makes little sense to me.It would be ok to output G(r) or r^2*G(r), but to output r*G(r) seems a mistake Thanks again,Marcelo PS: I did consider the spherical integration. On Aug 4, 2009, at 10:41 AM, Berk Hess wrote:Hi, You can look at the code yourself :) I coded this and -or (which I assume you are talking about) is G with 1/nm as a unit. It gives the probability that a particle has moved a distance r. The 1/nm is the normalization to make the values bin-size independent. Might it be that the difference in interpretation comes from if you consider normalization of the volume of sphere-shells or not? Berk From: c...@purdue.edu To: gmx-users@gromacs.org Date: Tue, 4 Aug 2009 10:25:33 -0400 Subject: [gmx-users] g_vanhove output Hi all, I believe there is a mistake in g_vanhove in version 4.0.5 The 'xvg' output file labels the y axis as G, with nm^-1 as units. From the units, I guessed that the output was actually r^2 G, however the initial slope is linear and not quadratic. After a few tries I concluded that the output is actually r*G, which is not something really useful. I wonder if someone could look at the code and confirm this doubt in one way or another. Many thank, Marcelo Carignano. PS: I couldn't find this on the list, but it has been difficult to access the archives lately. ___ gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php See all the ways you can stay connected to friends and family ___ 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 _ 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://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] Protein Activity
Hi How can I analyze / describe Protein Activity after MD simulation? Thank you Lin ___ 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] Pulling in GROMACS 4.0.3
Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: title= Martini cpp = /usr/bin/cpp integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 2500 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2500 nstvout = 2500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 33 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.4 ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Temperature coupling = tcoupl = V-Rescale ; Groups to couple separately = tc-grps = PROTEIN W ; Time constant (ps) and reference temperature (K) = tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 3.0 compressibility = 3e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 323 gen_seed = 666 constraints = none ; Type of constraint algorithm = constraint_algorithm = SHAKE ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 60 ; FREEZE GROUP ; freezegrps = freeze ; freezedim = Y Y Y ; Pulling pull= umbrella pull_geometry = distance pull_start = yes pull_nstxout= 10 pull_nstfout= 10 pull_ngroups= 1 pull_group0 = freeze pull_group1 = pull pull_init1 = 0.0 0.0 0.0 pull_rate1 = 5000.0 pull_k1 = 100 The reason why the number of time steps is quite small, the pull_rate quite high, and the force constant low is because I wanted to verify that the code actually works before doing the actual production run (around 13 ns). The issue I'm running into is that when I check the results using VMD, it seems almost as if the simulation ignored all of my pull commands. I changed the rate, force constant, and the # timesteps to many different values but to no avail. Every result seems to indicate that my pull commands were not read (nothing happens aside from vibration). I highly doubt that there is a bug (as mentioned in an earlier post). I don't know why this is happening. Is there something wrong with the code? I really appreciate the help! --Johnny - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ 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] Pulling in GROMACS 4.0.3
Johnny Lam wrote: Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: By pull apart, do you mean to unwind the secondary structure of the protein? If so, I don't think it will work. Doesn't MARTINI fix certain backbone parameters such that secondary structure remains very rigid over time? If that's the case, then the vibrations you're seeing are just the structure trying to resist being pulled apart. -Justin -- 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] Pulling in GROMACS 4.0.3
Hi Justin, Thx for the reply. By pull apart, I just wanted to expose an 'activation site' by using a force. It is somewhat similar to pulling two domains of a protein away from each other. I'm not aiming to undo any secondary structure. I hope this is clearer. Thanks again! --Johnny Johnny Lam wrote: Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: By pull apart, do you mean to unwind the secondary structure of the protein? If so, I don't think it will work. Doesn't MARTINI fix certain backbone parameters such that secondary structure remains very rigid over time? If that's the case, then the vibrations you're seeing are just the structure trying to resist being pulled apart. -Justin -- 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 - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ 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] Max notes = 256 ?
Hi But, I could not compile more than 256 notes when I run the Gromacs. Have anyone experienced compiling more than 1000 notes at one time? Thank you Lin ___ 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] Protein Activity
Hi Lin, Start with defining Protein activity. Tsjerk On Tue, Aug 4, 2009 at 8:11 PM, Chih-Ying Linchihying2...@gmail.com wrote: Hi How can I analyze / describe Protein Activity after MD simulation? Thank you Lin ___ gmx-users mailing list gmx-us...@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 -- 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://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] Pulling in GROMACS 4.0.3
Hi again, I actually figured it out. Turns out, it was a stupid formatting error in the .mdp file. Even though I had it as shown, it didn't read the pull command because it wasn't formatted properly (thought it was still a part of the first line). Sorry guys. --Johnny Hi Justin, Thx for the reply. By pull apart, I just wanted to expose an 'activation site' by using a force. It is somewhat similar to pulling two domains of a protein away from each other. I'm not aiming to undo any secondary structure. I hope this is clearer. Thanks again! --Johnny Johnny Lam wrote: Hi again, I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: By pull apart, do you mean to unwind the secondary structure of the protein? If so, I don't think it will work. Doesn't MARTINI fix certain backbone parameters such that secondary structure remains very rigid over time? If that's the case, then the vibrations you're seeing are just the structure trying to resist being pulled apart. -Justin -- 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 - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu - Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu ___ 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] Max notes = 256 ?
Chih-Ying Lin wrote: Hi But, I could not compile more than 256 notes when I run the Gromacs. Have anyone experienced compiling more than 1000 notes at one time? Do you mean nodes? There was a limit of 256 nodes in 3.2 or so, but in 4.0 there is no limit anymore. Thank you Lin ___ 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 -- 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 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ 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] MD Simulation Errors for Ethylene Glycol-Water System
Hello, I am trying to simulate a simple system of ethylene glycol (ethane-1,2-diol) solvated in a water box. I converted the pdb file to a mol2 file and used topolbuild 1.2.1 to generate topology files: $ topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 I the used editconf to enlarge the box. I then solvated the molecule using the following command: $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -box 3 3 3 -p ethanediol.top where ethanediol_box.gro is the structure of the molecule. I used grompp to generate the mdrun input file: $ grompp -f grompp.mdp -c ethanediol_solv.gro -p ethanediol.top -o ethanediol.tpr grompp.mdp is the following: title= Ethanediol cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 5 nstxout = 1 nstvout = 5 nstlog = 5 nstenergy= 10 nstxtcout= 1 xtc_grps = EDO SOL energygrps = EDO SOL nstlist = 10 ns_type = grid rlist= 0.8 coulombtype = cut-off rcoulomb = 1.4 rvdw = 0.8 tcoupl = Berendsen tc-grps = EDO SOL tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Berendsen tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds where EDO refers to ethylene glycol. grompp creates several notes: NOTE 1 [file grompp.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. NOTE 2 [file grompp.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. NOTE 3 [file grompp.mdp, line unknown]: This run will generate roughly 2500 Mb of data I then run the simulation: $ mdrun -s ethanediol.tpr -o traj.trr -x traj.xtc -v However mdrun produces several errors and warnings: t = 0.036 ps: Water molecule starting at atom 2659 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates t = 0.038 ps: Water molecule starting at atom 2659 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates t = 0.040 ps: Water molecule starting at atom 2659 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step 21 Warning: pressure scaling more than 1%, mu: 1.0372 1.0372 1.0372 Step 29, time 0.058 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.714709, max 3.541824 (between atoms 2 and 3) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 4 88.80.6606 0.6855 0.1520 2 3 90.60.4305 0.4542 0.1000 1 2 89.20.6123 0.4690 0.1435 5 6 93.40.4193 0.1741 0.1000 4 5 89.20.6156 0.5033 0.1435 === I am not sure where the errors are occuring (I am also wondering if the absence of explicit non-polar hydrogens in the .gro files are relevant). Please adivse. Thanks. Nancy ___ 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] Check out my photos on Facebook
Hi gmx-users@gromacs.org, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Dmitriy To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=1008503730k=Z3GX5X6YQ45AUCD1QB64RVXTVWFCr gmx-users@gromacs.org was invited to join Facebook by Dmitriy Golubovsky. If you do not wish to receive this type of email from Facebook in the future, please click on the link below to unsubscribe. http://www.facebook.com/o.php?k=7c1955u=10132975250mid=e2b636G5af318674a92G0G8 Facebook's offices are located at 1601 S. California Ave., Palo Alto, CA 94304 ___ 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] MD Simulation Errors for Ethylene Glycol-Water System
Nancy wrote: Hello, I am trying to simulate a simple system of ethylene glycol (ethane-1,2-diol) solvated in a water box. I converted the pdb file to a mol2 file and used topolbuild 1.2.1 to generate topology files: $ topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 I the used editconf to enlarge the box. I then solvated the molecule using the following command: $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -box 3 3 3 -p ethanediol.top where ethanediol_box.gro is the structure of the molecule. I used grompp to generate the mdrun input file: $ grompp -f grompp.mdp -c ethanediol_solv.gro -p ethanediol.top -o ethanediol.tpr grompp.mdp is the following: title= Ethanediol cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 5 nstxout = 1 nstvout = 5 nstlog = 5 nstenergy= 10 nstxtcout= 1 xtc_grps = EDO SOL energygrps = EDO SOL nstlist = 10 ns_type = grid rlist= 0.8 coulombtype = cut-off rcoulomb = 1.4 rvdw = 0.8 tcoupl = Berendsen tc-grps = EDO SOL tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Berendsen tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds where EDO refers to ethylene glycol. grompp creates several notes: NOTE 1 [file grompp.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. NOTE 2 [file grompp.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Take this advice. PME is substantially more accurate than plain cutoffs. Also, re-consider your values of the cutoffs (rcoulomb, rvdw). At the very least, rvdw is too short, given the specifics of the force field derivation. NOTE 3 [file grompp.mdp, line unknown]: This run will generate roughly 2500 Mb of data Ouch. Consider setting nstxout to some value considerably greater than 1, unless you need an exceptional amount of data. Since you have also set nstxtcout to 1, you almost certainly don't need your .trr file to be that huge :) Unrelated to your problem, but just FYI. I then run the simulation: $ mdrun -s ethanediol.tpr -o traj.trr -x traj.xtc -v However mdrun produces several errors and warnings: See the following: http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings http://oldwiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25 http://oldwiki.gromacs.org/index.php/blowing_up snip I am not sure where the errors are occuring (I am also wondering if the absence of explicit non-polar hydrogens in the .gro files are relevant). Please adivse. Not likely. It is a fundamental fact of UA force fields (like G53a6, as you have chosen) that non-polar hydrogens are not explicitly represented. These force fields work just fine. What have you done in terms of energy minimization and equilibration on this system? -Justin Thanks. Nancy ___ 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] topology info for specific bond between atoms in different molecules
Hi There, I am a new user of Gromacs and want to work on carbon nanotubes. I want to simulation carbon nanotube(cnt) bonded with polymers in water. And it will be much better to consider cnt and the bonded polymer as separate molecules, instead of one molecule. I can create the .itp file for both the nanotube and the polymer chain, and include them in the .top file. But I do not know how to describe the bond betwen the cnt and the polymer. Currently my .top file looks like this: (Thanks a lot!) *** [ defaults ] ; nbfunccomb-rulegen-pairs fudgeLJ fudgeQQ 11 [ atomtypes ] ; type mass charge ptype c6 c12 C 12.0 0.0 A0.00.0 X1.0e10 0.0 A0.00.0 OW15.994-0.82 A0.00.0 H 1.008 0.41 A0.00.0 ...more info [ nonbond_params ] ; aiaj funct aij bij C C 12.8768001E-34.691598E-6 OWOW 12.6169064E-32.633236E-6 COW 11.3176287E-31.388472E-6 ...more info [ bondtypes ] ; i j func b0 kb beta C C 3 0.1418 478.9 21.867 ...more info [ angletypes ] ;i j k func th0 cth C C C 2 120.0 562.2 ...more info [ dihedraltypes ] ; i jfunc phi0 cp mult C C 1 180.012.562 ...more info #include cnt_test.itp #include FLEXSPC.itp #include polymer.itp [ system ] CNT_H2O [ molecules ] CNT 1 SOL 1419 POL 2 * I read the manual and found an example that include bonds in topology file like below. The atom IDs are specified instead of atom type. Can I do this for atom (ID) in different molecules? Thanks. * [ bonds ] ; ai aj funct b0 kb 3 4 1 1.00e-01 3.744680e+05 3 5 1 1.00e-01 3.744680e+05 6 7 1 1.00e-01 3.744680e+05 6 8 1 1.00e-01 3.744680e+05 1 2 1 1.23e-01 5.020800e+05 1 3 1 1.33e-01 3.765600e+05 1 6 1 1.33e-01 3.765600e+05 * Regards, Stone___ 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] Regarding the 'hangs at atom 0' issue with x2top 4.x
Hi all, I've recently managed to reproduce the bug with x2top 4.x hanging at atom 0. The halt occurred when I was trying to generate a topology with the -pbc yes option (which is the default used unless you specify otherwise) using a structure file containing no information on the periodic box. As soon as I added the box info, x2top 4.0.4 did successfully generate a topology for me. I'm using x2top for periodic molecules (just forgot to add the box string this one time), so I didn't bother actually trying to turn off PBC, but I strongly suspect that this is the actual source of the problem reported by many colleagues on the list. Perhaps someone who previously complained about x2top 4.x halting should try first adding the -nopbc option to their command line and then adding the box vectors to their .gro and tell us all what happens then! :) Also, the developers might want to consider doing something about this setting and its default value. Aside from this one time, I've never had any problems with x2top 4.0.4 (especially with the -noparam option that I use all the time, just to keep things simple), and its value at generating topologies for my 2D periodic molecules cannot be overemphasized :) Hope this helps someone, Vasilii ___ 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] topology info for specific bond between atoms in different molecules
ucsd mail wrote: Hi There, I am a new user of Gromacs and want to work on carbon nanotubes. I want to simulation carbon nanotube(cnt) bonded with polymers in water. And it will be much better to consider cnt and the bonded polymer as separate molecules, instead of one molecule. I can create the .itp file for both the nanotube and the polymer chain, and include them in the .top file. But I do not know how to describe the bond betwen the cnt and the polymer. You cannot have a bonded interaction between atoms that belong to different [ moleculetype ] directives. So you will need to make a hybrid of the nanotube and the polymer. Depending on what sense you think it will be better to have them as separate molecules, you may wish to define index groups with make_ndx for whatever use you have in mind. Mark Currently my .top file looks like this: (Thanks a lot!) *** [ defaults ] ; nbfunccomb-rulegen-pairs fudgeLJ fudgeQQ 11 [ atomtypes ] ; type mass charge ptype c6 c12 C 12.0 0.0 A0.00.0 X1.0e10 0.0 A0.00.0 OW15.994-0.82 A0.00.0 H 1.008 0.41 A0.00.0 ...more info [ nonbond_params ] ; aiaj funct aij bij C C 12.8768001E-34.691598E-6 OWOW 12.6169064E-32.633236E-6 COW 11.3176287E-31.388472E-6 ...more info [ bondtypes ] ; i j func b0 kb beta C C 3 0.1418 478.9 21.867 ...more info [ angletypes ] ;i j k func th0 cth C C C 2 120.0 562.2 ...more info [ dihedraltypes ] ; i jfunc phi0 cp mult C C 1 180.012.562 ...more info #include cnt_test.itp #include FLEXSPC.itp #include polymer.itp [ system ] CNT_H2O [ molecules ] CNT 1 SOL 1419 POL 2 * I read the manual and found an example that include bonds in topology file like below. The atom IDs are specified instead of atom type. Can I do this for atom (ID) in different molecules? Thanks. * [ bonds ] ; ai aj funct b0 kb 3 4 1 1.00e-01 3.744680e+05 3 5 1 1.00e-01 3.744680e+05 6 7 1 1.00e-01 3.744680e+05 6 8 1 1.00e-01 3.744680e+05 1 2 1 1.23e-01 5.020800e+05 1 3 1 1.33e-01 3.765600e+05 1 6 1 1.33e-01 3.765600e+05 * Regards, Stone ___ 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] Different force field: Gromacs vs Autodock
Chih-Ying Lin wrote: Hi I use Gromacs (ffG45a3) to run MD in the protein vs ligand system. Then, I use Autodock to calculate the protein-ligand binding energy. As I know the force fields are different between ffG45a3 and Autodock. The two different force fields explain the same system. The two different force fields can be used to model the same system, yes. How can I explain this? I'm not sure what you're asking. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Max nodes = 256 ?
Chih-Ying Lin wrote: Hi So, which version of Gromacs is more reliable for compiling 1000 nodes now? And, which version with higher computation load per node = computation efficiency? 4.0 4.0.2 4.0.3 4.0.4 If you're making this choice, always use the most up-to-date version of the software (4.0.5). This way, you get the benefit of the most recent bug fixes and hence greater reliability. As far as running on 1000 nodes, performance will be largely dictated by your hardware. In my experience, there are no noticeable differences in speed between these minor releases. -Justin Thank you Lin Chih-Ying Lin wrote: Hi But, I could not compile more than 256 notes when I run the Gromacs. Have anyone experienced compiling more than 1000 notes at one time? Do you mean nodes? There was a limit of 256 nodes in 3.2 or so, but in 4.0 there is no limit anymore. Thank you Lin ___ 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] query regarding ffG43a1bon.itp
Hello I want to add a new bond streching parameter in the ffG43a1bon.itp file, Can anybody please tell me how the values under Examples of usage in terms of non-bonded atom types'' determined of each bond in the file ffG43a1bon.itp Subarna 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
