Re: [gmx-users] OPLS with Water models
Hi Justin, Thanks for the reply and the reference. I knew that I am asking for a broad question. OPLS will work for my protein problem. The reason why I am asking the question is to know how diffirent water models work for OPLS and is there any comparison work done for it. The reference you mentioned helps in some way. I will read more to teach myself about this broad question. Jianhui Date: Wed, 13 Apr 2011 15:50:49 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] OPLS with Water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4da5fe99.6020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi, This has been a long discussed question. But I am still not so clear after reading some posts and papers. What model should be used for OPLS-AA force field? Any consideration for the choice? Is SPC/E a good one? Michael shirts has said in http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html Jorgensen's OPLS-AA (and more recent OPLS-AA/L) force fields were developed almost completely with TIP4P water. Also, David van der spoel had a paper with Erik Lindahl (JPCB 2003, 117, 11178-11187) confirming: OPLS works better with TIP4P. However, many simulations using OPLS with SPC or TIP3P. Alan Wilter S. da Silva said in http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.htmlthat I did short tests with spce and I got a paper with Dr. der Spoel. But I can not find any paper for OPLS-AA and SPC/E water. Suggestions or references are welcomed. Well, there's this one that endorses SPC/E for several properties: http://dx.doi.org/10.1021/jp0641029 What you've asked is extremely broad. Different force fields and solvent models can be combined in a number of ways to measure various quantities. It all comes down to what you're hoping to measure. Is it protein conformational sampling? Reproducing NMR signals? Hydration energies or other thermodynamic properties? Then there's the complication of whether or not OPLS-AA is inherently the best choice to represent your protein for these endeavors. There has been a wealth of recent literature on force field comparisons for protein dynamics, as well. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OPLS with Water models
Hi, This has been a long discussed question. But I am still not so clear after reading some posts and papers. What model should be used for OPLS-AA force field? Any consideration for the choice? Is SPC/E a good one? Michael shirts has said in http://lists.gromacs.org/pipermail/gmx-users/2002-July/002007.html Jorgensen's OPLS-AA (and more recent OPLS-AA/L) force fields were developed almost completely with TIP4P water. Also, David van der spoel had a paper with Erik Lindahl (JPCB 2003, 117, 11178-11187) confirming: OPLS works better with TIP4P. However, many simulations using OPLS with SPC or TIP3P. Alan Wilter S. da Silva said in http://lists.gromacs.org/pipermail/gmx-users/2003-February/004315.html that I did short tests with spce and I got a paper with Dr. der Spoel. But I can not find any paper for OPLS-AA and SPC/E water. Suggestions or references are welcomed. Thanks. Jianhui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ACPYPE download
I did find this page and followed the instructions. But I can not download it. JH Date: Mon, 17 Jan 2011 06:47:35 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] ACPYPE download To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d334b57.7050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 17/01/2011 5:05 AM, Jianhui Tian wrote: Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone who has successful experience using ACPYPE and would be willing to provide me the program? Did you find this page? http://code.google.com/p/acpype/wiki/HowToUse 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ACPYPE download
Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone who has successful experience using ACPYPE and would be willing to provide me the program? Thanks a lot. JH -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
Date: Fri, 31 Dec 2010 19:08:50 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d1e7092.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] electron density
Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Jianhui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Job crash: checkpoint file
Dear GMX users, I am running a replica simulation and the job crashed with the following message: File input/output error: Cannot rename checkpoint file; maybe you are out of quota? From the mailling list, I see this might be a permission problem. However, I checked the file permission and nothing wrong was noticed. If I rerun the crashed simulation, it goes through the second time. This seems strong. Any suggestion is welcomed. JH -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM - gromacs epsilon and sigma conversiion
eps(charmm)*4.184=epsilon(Gromacs) 0.15*4.184=0.6276 Rmin/2(Charmm)*2/(2^1/6)=sigma(Gromacs) 2.27*2/(2^(1/6))=0.404468(nm) Cheers, Jianhui Date: Fri, 24 Sep 2010 15:55:44 +0200 From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] CHARMM - gromacs epsilon and sigma conversiion factors To: gmx-users@gromacs.org Message-ID: f654b3ee96986e4b8dc6ef0919c88da301038...@loderi.intra.cea.fr Content-Type: text/plain; charset=iso-8859-1 Hi all, I would like to add new atom types in the charmm27.ff for futures simulations of glyolipids in water with gmx 4.5.1. I have finished to convert the bonded in GROMACS format. However, I am little puzzled with the vdW paramaters. I would like to know how to convert them (i.e. what are the conversion factors used to convert the CHARMM sigma and epsilon parameters to gromacs sigma and epsilon values ?). For example for the chloride atom CLA CHARMM 27 ; atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 CLA 0.0 -0.150 2.27 ! chloride GROMACS ffcharmmnb.itp ;name at.num mass charge ptype sigma epsilon CLA 17 35.45 -1.00 A 0.404468018036 0.6276 Thanks in advance for your help Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem after tranferred CHARMM c36 to Gromacs
Dear GMX users, I am interested in using CHARMM c36 force field in Gromacs. I wrote a script to generate the ffcharmmbon.itp, ffcharmmnb.itp and molecule.itp file. After that, I compared the energy terms from Gromacs and NAMD. The bond, angle, dihedral, improper and electrostatic energy terms all agree well. However, there are big difference for VDW energy terms. Does anyone have any hint for what might be wrong? Thanks a lot. JH -- 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] Problem after tranferred CHARMM c36 to Gromacs
Previously in gromacs, if you use Ryckaert-Bellemans type dihedrals, you must erase the 1-4 pairs. Now for 4.5-beta3 dihedral function type 9, how do you deal with the 1-4 pairs? Thanks. JH -- Forwarded message -- From: Jianhui Tian jianhuit...@gmail.com Date: Fri, Sep 3, 2010 at 10:17 AM Subject: Problem after tranferred CHARMM c36 to Gromacs To: gmx-users@gromacs.org Dear GMX users, I am interested in using CHARMM c36 force field in Gromacs. I wrote a script to generate the ffcharmmbon.itp, ffcharmmnb.itp and molecule.itp file. After that, I compared the energy terms from Gromacs and NAMD. The bond, angle, dihedral, improper and electrostatic energy terms all agree well. However, there are big difference for VDW energy terms. Does anyone have any hint for what might be wrong? Thanks a lot. JH -- 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] CHARMM c36 to Gromacs
Hi, Gromacs 4.5-beta3 explicitly include the CHARMM c27 force field but not the c36 force field. Have anyone done any work to transfer the CHARMM c36 force field to Gromacs? Dr. Mark James Abraham has written a perl script to do the charmm_to_gromacs transfer, however that only works for the c27 which is already included in Gromacs. Thanks a lot JH -- 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] dihedral function type 9 in rtp file
Hi, In the rtp file of Gromacs version 4.5-beta3, the dihedral function type for proper dihedrals is 9. However, I can't find any documentation about the function form of this function type. Also, you can add multiple dihedral potentials for one dihedral term explicitly in the rtp file. The term is: [ dihedrals ] ; optional ;atom1 atom2 atom3 atom4 phi0 cp mult What is the function form here? Thanks. Jianhui -- 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] dihedral function type 9 in rtp file
Thanks Dallas. Forgot to search the mailing list this time. Jianhui Date: Thu, 26 Aug 2010 08:39:17 +1000 From: Dallas Warren dallas.war...@monash.edu Subject: RE: [gmx-users] dihedral function type 9 in rtp file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 39d19992d8a3804b8c801976acb4596247e...@prk-exch-01.vcp.local Content-Type: text/plain; charset=us-ascii http://lists.gromacs.org/pipermail/gmx-users/2010-August/053255.html Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] carbohydrate parameters in ffG53a6
Hi Parichita, Thanks for the suggestion. However, the question is what parameters from ffG53a6 can be used for not included sugars or glycolipid. I guess you can not simply use the charge, angle and dihedral values based on the atom types from 53a6. Jianhui Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST) From: parichita parichita parichitamajum...@yahoo.co.in Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 456742.75700...@web8903.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi Jianhui, For your sugar part you can use PRODRG, which will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS and from literature if you can find out the parameters of ffG53a6 force field, then you can correct the charge, angle and dihedral values that you are collected from the PRODRG. Hope this will help you. Regards... Parichita... Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. --- On Wed, 18/8/10, Jianhui Tian jianhuit...@gmail.com wrote: From: Jianhui Tian jianhuit...@gmail.com Subject: [gmx-users] carbohydrate parameters in ffG53a6 To: gmx-users@gromacs.org Date: Wednesday, 18 August, 2010, 10:16 AM Hi, I want to do some simulations about carbohydrates and glycolipid. In the ffG53a6.rtp file, I just see limited parameters for carbohydrate, like monosaccharide Glucose, Mannose and Galactose. What parameters can be used for others like arabinose? Also, is there any parameters available in the Gromacs force field for glycolipid? Jianhui -- 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] carbohydrate parameters in ffG53a6
Hi Justin, I compare the few sugars (Glc, Gal, Man), their parameters are indeed nearly identical except for some improper dihedrals. Then I can transfer these parameters to other sugars. How about Glycolipid? For example, the link phosphatidyl-myo-inositol. Do you have any suggestion? Thanks. Jianhui Date: Wed, 18 Aug 2010 12:45:15 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c6c0e1b.1020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi Parichita, Thanks for the suggestion. However, the question is what parameters from ffG53a6 can be used for not included sugars or glycolipid. I guess you can not simply use the charge, angle and dihedral values based on the atom types from 53a6. Gromos building blocks are quite transferable between different molecules. Compare a few sugars - the parameters are nearly identical. That is one of the central features of this particular force field, that functional group charges should be as versatile as possible. As for the lipids, there are new versions of 53A6 (which I believe have been uploaded to the Gromacs site) that perform substantially better than the built-in parameters. The long acyl chains are not particularly accurate in the default 53A6. -Justin Jianhui Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST) From: parichita parichita parichitamajum...@yahoo.co.in mailto:parichitamajum...@yahoo.co.in Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 456742.75700...@web8903.mail.in.yahoo.com mailto:456742.75700...@web8903.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi Jianhui, For your sugar part you can use PRODRG, which will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS and from literature if you can find out the parameters of ffG53a6 force field, then you can correct the charge, angle and dihedral values that you are collected from the PRODRG. Hope this will help you. Regards... Parichita... Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. -- 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] carbohydrate parameters in ffG53a6
Hi, I want to do some simulations about carbohydrates and glycolipid. In the ffG53a6.rtp file, I just see limited parameters for carbohydrate, like monosaccharide Glucose, Mannose and Galactose. What parameters can be used for others like arabinose? Also, is there any parameters available in the Gromacs force field for glycolipid? Jianhui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: trjcat -demux problem
I solved the problem. The command that works is: trjcat -f md00.xtc md01.xtc ... md0N.xtc -o out00.xtc out01.xtc ... out0N.xtc -s replica_index.xvg Jianhui Date: Tue, 03 Nov 2009 10:24:12 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: [gmx-users] Re: trjcat -demux problem To: Jianhui Tian ti...@rpi.edu, Gromacs Users' List gmx-users@gromacs.org Message-ID: 4af04b1c.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Please keep all correspondence on the gmx-users list. I do not advertise myself as a private help service, and furthermore, you always stand a better chance at getting a response by posting to the list. Is this the post you're referring to? http://lists.gromacs.org/pipermail/gmx-users/2008-December/038719.html It's always best to refer directly to the thread you read. What version of Gromacs are you using? I seem to recall that the quoted error came up in 3.3.3, but not in the 4.0.x series. I never actually solved the above problem; my issue was with version 4.0.2, and it ended up being my own fault for using an improper command :) -Justin Jianhui Tian wrote: Hi Justin, I found your post on gromacs mailing list when I searched for the trjcat -demux problem. I had the same problem as you had before: Fatal error: Demuxing the same replica 4 twice at time 30.02 Unfortunately, I didn't find any successful hit to solve it on the mailing list. Could you please share with me how to solve the problem if you have solved it? Thank you very much. Jianhui ___ 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] multiple processor running of gromacs-4.0.4
Hi Mark, You are right that treating electrostatics and vdw without cutoff and use multiple processors to speed up doesn't make any sense. Using cutoff for electrostatics and vdw without using pbc and pme, the system can't run on parallel (using flag -pd doesn't work either), but works on single node. Using cutoff for electrostatics and vdw with pbc and pme, the system can run on parallel. Thanks for the clarifications. Jianhui Jianhui Tian wrote: Hi, I have a small system of fullerene ball with waters. I want to simulation the system without pbc and pme, treating the coulomb and vdw without cutoff. The system can be run on single processor. But when I try to run it with multiple processors, it can't proceed. I am including the error message at the end of this mail. Those messages are generic failure messages from the MPI system. The stack trace therein suggests you should read the stderr and/or log file to get some diagnostic information from GROMACS. Possibly your system is blowing up because you've started from an unsuitable configuration. There are some of my guesses for the possible reason of the error: 1. Do we have to use pbc and pme to use multiple processors for simulation? Wouldn't think so. However because you have no cut-offs, there will be no advantage to DD because there is no data locality - every processor needs the position of every atom. mdrun -pd may work. It strikes me as possible that this scenario doesn't work in parallel on GROMACS. 2. Can wen use restraints when use multiple processors? Yes. 3. If a molecule is divided into two parts in domain decomposition, will this be a problem for simulation? No, that's routine. Mark Thanks for any suggestion about this error message. logfile:-- [0,1,1]: OpenIB on host compute-1-12.local was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -- -- [0,1,0]: OpenIB on host compute-1-12.local was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -- NNODES=2, MYRANK=0, HOSTNAME=compute-1-12.local NODEID=0 argc=13 NNODES=2, MYRANK=1, HOSTNAME=compute-1-12.local NODEID=1 argc=13 . . . . Reading file /data/disk04/tianj/trp_remd_091012/equilibrium/test/trp_full_run1.tpr, VERSION 4.0 (single precision) [compute-1-12:08033] *** Process received signal *** [compute-1-12:08033] Signal: Segmentation fault (11) [compute-1-12:08033] Signal code: Address not mapped (1) [compute-1-12:08033] Failing at address: 0xc0 [compute-1-12:08033] [ 0] /lib64/libpthread.so.0 [0x378fe0de80] [compute-1-12:08033] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x39) [0x378f642309] [compute-1-12:08033] [ 2] /lib64/libc.so.6(_IO_fprintf+0x88) [0x378f64cf68] [compute-1-12:08033] [ 3] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mk_mshift+0x315) [0x516593] [compute-1-12:08033] [ 4] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x45fa97] [compute-1-12:08033] [ 5] /usr/local/gromacs-4.0.4/bin/mdrun_sm(dd_bonded_cg_distance+0x36c) [0x45ff53] [compute-1-12:08033] [ 6] /usr/local/gromacs-4.0.4/bin/mdrun_sm(init_domain_decomposition+0x780) [0x44d10c] [compute-1-12:08033] [ 7] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mdrunner+0x89c) [0x429f6e] [compute-1-12:08033] [ 8] /usr/local/gromacs-4.0.4/bin/mdrun_sm(main+0x7ba) [0x4306b6] [compute-1-12:08033] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x378f61d8b4] [compute-1-12:08033] [10] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x4199a9] [compute-1-12:08033] *** End of error message *** mpirun noticed that job rank 0 with PID 8033 on node compute-1-12.local exited on signal 11 (Segmentation fault). 1 additional process aborted (not shown) ___ 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] multiple processor running of gromacs-4.0.4
Hi, I have a small system of fullerene ball with waters. I want to simulation the system without pbc and pme, treating the coulomb and vdw without cutoff. The system can be run on single processor. But when I try to run it with multiple processors, it can't proceed. I am including the error message at the end of this mail. There are some of my guesses for the possible reason of the error: 1. Do we have to use pbc and pme to use multiple processors for simulation? 2. Can wen use restraints when use multiple processors? 3. If a molecule is divided into two parts in domain decomposition, will this be a problem for simulation? Thanks for any suggestion about this error message. logfile:-- [0,1,1]: OpenIB on host compute-1-12.local was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -- -- [0,1,0]: OpenIB on host compute-1-12.local was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -- NNODES=2, MYRANK=0, HOSTNAME=compute-1-12.local NODEID=0 argc=13 NNODES=2, MYRANK=1, HOSTNAME=compute-1-12.local NODEID=1 argc=13 . . . . Reading file /data/disk04/tianj/trp_remd_091012/equilibrium/test/trp_full_run1.tpr, VERSION 4.0 (single precision) [compute-1-12:08033] *** Process received signal *** [compute-1-12:08033] Signal: Segmentation fault (11) [compute-1-12:08033] Signal code: Address not mapped (1) [compute-1-12:08033] Failing at address: 0xc0 [compute-1-12:08033] [ 0] /lib64/libpthread.so.0 [0x378fe0de80] [compute-1-12:08033] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x39) [0x378f642309] [compute-1-12:08033] [ 2] /lib64/libc.so.6(_IO_fprintf+0x88) [0x378f64cf68] [compute-1-12:08033] [ 3] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mk_mshift+0x315) [0x516593] [compute-1-12:08033] [ 4] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x45fa97] [compute-1-12:08033] [ 5] /usr/local/gromacs-4.0.4/bin/mdrun_sm(dd_bonded_cg_distance+0x36c) [0x45ff53] [compute-1-12:08033] [ 6] /usr/local/gromacs-4.0.4/bin/mdrun_sm(init_domain_decomposition+0x780) [0x44d10c] [compute-1-12:08033] [ 7] /usr/local/gromacs-4.0.4/bin/mdrun_sm(mdrunner+0x89c) [0x429f6e] [compute-1-12:08033] [ 8] /usr/local/gromacs-4.0.4/bin/mdrun_sm(main+0x7ba) [0x4306b6] [compute-1-12:08033] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x378f61d8b4] [compute-1-12:08033] [10] /usr/local/gromacs-4.0.4/bin/mdrun_sm [0x4199a9] [compute-1-12:08033] *** End of error message *** mpirun noticed that job rank 0 with PID 8033 on node compute-1-12.local exited on signal 11 (Segmentation fault). 1 additional process aborted (not shown) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Large fullerene ball simulations
Hi, I want to do some simulation about large fullerene balls. I searched the website and searched the mailing list. The largest fullerene ball I can get is C2160. But I want some larger ones like C3840 or so. Does anyone have any information about the coordinates and topology of large fullerene balls. Thanks. Jianhui ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: shake block problem
Hi GMX-Users, Does anyone have any idea about the problem? Thanks a lot in advance. I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _ splitting topology... Walking down the molecule graph to make shake-blocks There are 24390 charge group borders and 26054 shake borders There are 24390 total borders Division over nodes in atoms: 21234 21234 --- Program grompp_d, VERSION 3.3 Source code file: splitter.c, line: 121 Fatal error: Shake block crossing node boundaries constraint between atoms (21226,21234) --- I used h-bonds constraints. I tried not to without constraints and the system can be ran on 2 processors well, but the time-step is small then. please submit a bugzilla and upload your input files (top, gro, mdp). Hi David, There are the mdp file and the errors in the following: The mdp file: _ title= ps md at 300 K, 1 bar cpp = /lib/cpp include = -I../top define = integrator = md tinit= 0.0 dt = 0.001 nsteps = 5 nstxout = 500 nstvout = 500 nstlog = 500 nstenergy= 500 energygrps = AOTs Cores ICTs nstlist = 1 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = pme rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 DispCorr = no tcoupl = Berendsen tc_grps = AOTs Cores ICTs tau_t= 0.5 0.5 0.5 ref_t= 300.0 300.0 300.0 pcoupl = berendsen pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no constraints = h-bonds constraint_algorithm = shake Errors: _ Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.119 0.119 0.119 splitting topology... Walking down the molecule graph to make shake-blocks There are 24210 charge group borders and 25874 shake borders There are 24210 total borders Division over nodes in atoms: 21078 21078 --- Program grompp_d, VERSION 3.3 Source code file: splitter.c, line: 121 Fatal error: Shake block crossing node boundaries constraint between atoms (21070,21078) --- You Think That You're Bigger When You Fill the Void (Urban Dance Squad) NNODES=2, MYRANK=0, HOSTNAME=compute-3-15.local NNODES=2, MYRANK=1, HOSTNAME=compute-3-15.local NODEID=1 argc=11 NODEID=0 argc=11 _ _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] shake-block problem
Hi GMX-Users, Does anyone have any idea about the problem? Thanks a lot in advance. I got an error message when using gromacs on 2 processors on the same computer.The error message is like this:_splitting topology... Walking down the molecule graph to make shake-blocksThere are 24390 charge group borders and 26054 shake bordersThere are 24390 total bordersDivision over nodes in atoms: 21234 21234--- Program grompp_d, VERSION 3.3Source code file: splitter.c, line: 121Fatal error:Shake block crossing node boundariesconstraint between atoms (21226,21234)--- I used h-bonds constraints.I tried nottowithout constraintsand the system can be ran on 2 processors well, but the time-step is small then. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Coulomb 1-4 interactions
Hi gmx-users: I am running a comparison between AMBER and Gromacs for a AOT system. First I createdthe AMBER force field and then transformed it to Gromacs force field. I did 1 step of MDrespectively in AMBER and Gromacs with the same configuration. All the energy terms including bond, angle, dihedral, LJ (SR), LJ (14) and Coulomb (SR) arethe samewith each otherbetween the two runs except the Coulomb(14) interaction. What might be the reason for this? I have totally no idea. Because the LJ (14) and Coulomb(14) calculation use the same 1-4 pairs in Gromacs, the LJ (14)is the same which means the 1-4 pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the same which means the charges are the same between AMBER and Gromacs. (I also checked these two things explicitly between AMBER and Gromacs.) How could the Coulomb (14) be different then? Does any one have any idea about how the coulomb (14) interactions are calculated in AMBER and Gromacs? Thanks a lot. Best Regards, Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Questions about water in Gromacs
Hi, Thank you for the suggestions. The water numbers should be fine. Becuase I can run the same system in AMBER ok. I have done minimization. And the system explodes during the equilibrium process. I compared the energy of different component between AMBER and Gromacs. For all these components,BOND energy always has big difference for the same component between AMBER ang Gromacs. While the ANGLE, DIHEDRAL andLJ etcare consistent with each other.I can't figure out why. Thanks. Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 water in Gromacs
Dear gmx-users: I am now studying a reverse micelle system using Gromacs. The system is like this: Isooctane outside, AOT reverse micelle in the center and water core inside the reverse micelle. I didn't use standard Gromacs force field, instead I am using a force field transferred from CHARMM following the *.itp format. The problem is like this: when you run the MD, the AOT reverse micelle will explode instead of holding there as a reverse micelle and the water core seems to be distributed evenly in the system. I checked the force field to make sure there is nothing wrong with it. I wonder whether the problem is caused because water molecules are labelledasSOL in gromacs, so the water tends to be uniformally distributed. Does the label SOL just a label or it is really treated as solvent? Thank you very much. Best regards, Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
