Re: [gmx-users] backup files
Thanks for you reply but, I'm afraid it doesn't work with me! In fact, if I write more \#conf.gro# I can read from this file. However, when using it as input for gromacs utilities the programs complain of input error. cp #conf.gro# good.gro ___ 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] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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] Gromacs 3.3.1 vs SegFault
Hi all. I`m trying to make short MD simulation in tRNA+water+ions(Na+) system. But mdrun fails with Segmentaiont Fault. I can`t fix it, please help, if it`s possible. Gromacs version: 3.3.1 Forcefield: ffamber99p. Stas Bobritsky, student. ___ 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] about PMF calculation
Hi gmx-users I am a gromacs beginner, I want to do the PMF calculation ,I have done as the manual said ,I added the ppa, ndx files and got a pdo file . But I don't know what to do with this pdo file. Can anyone tell me what should I do if I want to calculate the PMF? Thanks in advance. Yongqi Huang --黄永棋 --- 猜大小单双 16种赚钱的好方法，狂猜狂赚( http://ad4.sina.com.cn/sina/limeng3/mail_zhuiyu/2007/mail_zhuiyu_20070315.html ) === 注册新浪2G免费邮箱（ http://mail.sina.com.cn/chooseMode.html ）___ 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] freezing/position restraints and minimization
Hmm, interesting... And what about the -DFLEXIBLE definition in your mdp file during steepest descent minimization? Do you know if that will also deform your (SPC) water molecules? And will that deformation be corrected again during the first equilibration step(s)? I ask this, because I read on severel places (e.g. the online mdp options manual and in one of the tutorials) that you could use the - DFLEXIBLE definition to allow steepest descent to minimize further. So I've used it for most of my minimizations up til now, assuming that was the right thing to do. Thanks, Jeroen On 17 Mar 2007 at 12:00, David Mobley wrote: Sorry to e-mail so much. But it seems this is, indeed, the problem. For freeze groups to work in minimization you need to use a minimizer which is can handle constraints properly. In GROMACS the only minimizer that is set up to handle constraints properly is steepest descents. Note that this also has implications for anyone using rigid water models (most of us): If you're minimizing with L-BFGS or other minimizers aside from steepest descents, you're probably deforming your water molecules, as well. David ___ 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
回复： [gmx-users] about PMF calculation
try mdrun_d and g_wham: Can you tell me how to produce pdo file? thank you very much! 黄永棋 [EMAIL PROTECTED] 写道： Hi gmx-users I am a gromacs beginner, I want to do the PMF calculation ,I have done as the manual said ,I added the ppa, ndx files and got a pdo file . But I don't know what to do with this pdo file. Can anyone tell me what should I do if I want to calculate the PMF? Thanks in advance. Yongqi Huang -- 黄永棋 --- 猜大小单双 16种赚钱的好方法，狂猜狂赚( http://ad4.sina.com.cn/sina/limeng3/mail_zhuiyu/2007/mail_zhuiyu_20070315.html ) === 注册新浪2G免费邮箱（ http://mail.sina.com.cn/chooseMode.html ）___ gmx-users mailing list gmx-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 - Mp3疯狂搜-新歌热歌高速下 ___ 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] freezing/position restraints and minimization
Jeroen van Bemmelen wrote: Hmm, interesting... And what about the -DFLEXIBLE definition in your mdp file during steepest descent minimization? Do you know if that will also deform your (SPC) water molecules? And will that deformation be corrected again during the first equilibration step(s)? I ask this, because I read on severel places (e.g. the online mdp options manual and in one of the tutorials) that you could use the - DFLEXIBLE definition to allow steepest descent to minimize further. So I've used it for most of my minimizations up til now, assuming that was the right thing to do. it is fine, but your bond lengths and bond angle in water will be slightly off the equilibrium values. This will be corrected during th eequilibration. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Hi. g_hbond can do that, sort of. You can calculate e.g. the nr of water oxygens within a certain distance from the protein. The limitation lies in that g_hbond operates at a atom basis, not molecule, meaning that there is strictly no way of finding the number of solvent molecules directly. However, I think that counting the nr of water oxygens would be good enough for most applications. /Erik 17 mar 2007 kl. 11.17 skrev OZGE ENGIN: Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ 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] Adding a new force field to Gromacs
Actually it is about to add a new form of potential energy function. A quick but dirty method is to user User Table for NB interaction. Check it from the manual. Regards, Yang Ye Tandia, Adama wrote: Dear ALL: Is it documented somewhere how can one add a new non-bonded force field into Gromacs? I'm interested on adding the Stillinger-Weber force field, with two and three body contributions. Has anyone ever tried this before? Thanks in advance for your answers. Best wishes, Adama == Adama Tandia Modeling Simulation Corning INC USA Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___ 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 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] Restarting a gromacs calcluation
Milan Melichercik wrote: Dňa Pi 16. Marec 2007 14:19 Triguero, Luciano O napísal: Dear Users, Thank for your help. I started a 10 ns simulation, but it dies because of an error in the cluster PBS system, so I want to continue the simulation from the last (r,v) point. May I still use tpbconv to restart from that last point and continue the simulation. Check where your trr or edr file ends using gmxcheck -f or -e. The shorter will be used by tpbconv for your new tpr. Specify tpbconv with -f and -e. Sure - as far as I know. It will generate new .tpr, which you will use for starting the simulation - when it is finished, simply concatenate trajectories, energy files with trjcat and eneconv. Milan Thank again, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 From: [EMAIL PROTECTED] on behalf of Yang Ye Sent: Fri 3/16/2007 8:49 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Restarting a gromacs calcluation Can you be more specific? Continue or start new simulation. Use tpbconv to extend your simulation. On 3/16/2007 9:37 AM, Triguero, Luciano O wrote: Dear users, How do I restart a gromacs simulation? Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 ___ 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 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 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 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] oplsaa with tip4p
Create the top for the protein alone. Then insert #include tip4p.itp and add new entries under [ molecules ] section Regards, Yang Ye Christian Seifert wrote: Hi. I want to use the ff oplsaa with tip4p water (as suggested in the manual). Using: genbox_d -cp hpo4_box.pdb -o hpo4_water.pdb -cs tip4p.gro creates a good pdf-file with tip4p-water, but the following: pdb2gmx_d -f hpo4_water.pdb -o hpo4_water.gro -p hpo4_water.top -ff oplsaa -n hpo4_water.ndx -water tip4p brings up this error: --- Program pdb2gmx_d, VERSION 3.3.1 Source code file: pdb2gmx.c, line: 393 Fatal error: Atom MW in residue HO4 1 not found in rtp entry with 4 atoms while sorting atoms --- Is there any workaround? Thanks in advance Christian Seifert. ___ 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 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] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
try g_trjorder. Some code modification may be needed. Regards, Yang Ye OZGE ENGIN wrote: Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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 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] Adding a new force field to Gromacs
Yang Ye wrote: Actually it is about to add a new form of potential energy function. A quick but dirty method is to user User Table for NB interaction. Check it from the manual. Regards, Yang Ye Tandia, Adama wrote: Dear ALL: Is it documented somewhere how can one add a new non-bonded force field into Gromacs? I'm interested on adding the Stillinger-Weber force field, with two and three body contributions. Has anyone ever tried this before? Thanks in advance for your answers. Except that gromacs can not do three body nonbonded interactions. It wouldn't be very hard to add the force calculations, but the input would be slightly more involved. If you want to do this yourself then we should move this thread to the developers mailing list. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] Fatal error when using Hbond restraints
Robert Johnson wrote: Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and DNA that require hydrogen bond restraints. However, I'm getting the following error when trying to run the system across several nodes: Fatal error: Shake block crossing node boundaries constraint between atoms (1680,1716) The atoms listed are in the substrate. Since I'm already restraining the substrate atoms, I don't really need to constrain the Hbonds in the SiO2. Is there any way to apply Hbond restraints only to a group of atoms? Alternatively, how does Gromacs decide which bonds contain hydrogen? I could just alter the topology file for the substrate to trick Gromacs into thinking that the hydrogens in the SiO2 are really a different type of atom. Thanks, Bob Johnson I'm at this very moment looking at http://bugzilla.gromacs.org/show_bug.cgi?id=110 which reports the same error. You might try to use pbc=full and contraint_algorithm = lincs to circumvent the problem. The problem you have does not arise from the position restraints though, and, by the way, you probably don't need those restraints at all. I don't know what you mean with hbond restraints though... -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] Fatal error when using Hbond restraints
Robert Johnson wrote: Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and DNA that require hydrogen bond restraints. However, I'm getting the following error when trying to run the system across several nodes: Fatal error: Shake block crossing node boundaries constraint between atoms (1680,1716) The atoms listed are in the substrate. Since I'm already restraining the substrate atoms, I don't really need to constrain the Hbonds in the SiO2. Is there any way to apply Hbond restraints only to a group of atoms? Alternatively, how does Gromacs decide which bonds contain hydrogen? I could just alter the topology file for the substrate to trick Gromacs into thinking that the hydrogens in the SiO2 are really a different type of atom. Thanks, Bob Johnson ___ 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 Bob, try using constraints = all-bonds, or make sure that your charge groups overlap with the constraint groups. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Thank you very much for your attention! Best regards, Ozge Engin -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 18 Mar 2007 00:35:13 +0800 Subject: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule try g_trjorder. Some code modification may be needed. Regards, Yang Ye OZGE ENGIN wrote: Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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 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 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] problem regarding mdrun and g_hbond
Hi David, Of course, it's not a dogma... But in your case, it will be well thought over. That makes the difference. (From another point of view, if the simulation system is small, often you'll still want temperature coupling anyway...). Anyway, as with all gromacs warnings, they should just make you think about the things you're doing. If you know it's what you want, you can always ignore'm. Tsjerk On 3/16/07, David van der Spoel [EMAIL PROTECTED] wrote: Mark Abraham wrote: I think a warning is a good idea, but maybe 10 is even on the low side for that. Since temperature is macroscopic, you'll need enough atoms not to deviate too much from the target temperature. I have no evidence on which I can make a proper suggestion... My bidding will be 50! Going once, going twice... (maybe someone has looked more into this matter. David, Berk?). I added a bugzilla enhancement-request for this feature, suggesting that if the user tries 3+ T-coupling groups where the smallest is less than 10% of the smaller of the other two then we probably have a case of bad planning from the user, and should give a warning. Doubtless there are better ideas out there... it's after midnight here! I've implemented the 10% of atoms test. Could be changed to a fixed number of atoms as well. Not sure which one makes more sense (I quite often simulate systems that fall under the fixed atom limit (didn't Tsjerk say 50?)). -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] POPC membrane simulation (popc.itp)
Hi all: I ´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site) and i want to do a popc.itp file using ffG53a5 force field. Some days ago i was working with dppc membranes and i took one lipid and run it through pdb2gmx, using my favourite force field and include the dppc.itp file in my .top file, but i know that the topology of popc lipid isn´t in the database of gromacs. I ´ve obtained the popc.itp (one lipid) of the PRODRG server, but the conformation is bad, i note that when i visualize it in VMD and i analyze some parameters. Also the atom types are different. I think i can to converter the dppc.itp file in popc.itp file, but i don´t know what to do. Should i take the topology of dppc lipid and modified it including some atoms of the oleoil chain of the popc lipid (CA1 y CA2 atoms)? Can i find the parameters of the similar bounds of the last atoms and include it in the dppc.itp file? Could anybody help me? Thank you for your time Maite ___ 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] Restarting a gromacs calcluation
Dear Users, Thank for your help. I started a 10 ns simulation, but it dies because of an error in the cluster PBS system, so I want to continue the simulation from the last (r,v) point. May I still use tpbconv to restart from that last point and continue the simulation. Check where your trr or edr file ends using gmxcheck -f or -e. The shorter will be used by tpbconv for your new tpr. Specify tpbconv with -f and -e. Dear, Thank for your answer. I still have a problem. Do you mean (-f and -e) or (-f or -e) I checked my trr and edr files and edr files ends first, then I typed: tpbconv -s md_input.tpr -f .trr -e .edr -o md_cont.tpr and got the following error message: ++ Opened md_minim_energy.edr as single precision energy file Reading frame 4000 time 4000.000 Last frame read 4876 WARNING: Incomplete frame: nr 4877 time 4876.000 --- Program tpbconv, VERSION 3.3.1 Source code file: enxio.c, line: 401 Fatal error: Could not find frame with time 4884.00 in 'md_minim_energy.edr' +++ However, tpbconv runs without error when I provide only option -e .edr. Is it correct to restart a calculation with the .tpr file generated with only -e .edr option. Will be then possible to concatenate trajectories correctely? Advices, Thank for your time, Luciano Sure - as far as I know. It will generate new .tpr, which you will use for starting the simulation - when it is finished, simply concatenate trajectories, energy files with trjcat and eneconv. Milan Thank again, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 From: [EMAIL PROTECTED] on behalf of Yang Ye Sent: Fri 3/16/2007 8:49 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Restarting a gromacs calcluation Can you be more specific? Continue or start new simulation. Use tpbconv to extend your simulation. On 3/16/2007 9:37 AM, Triguero, Luciano O wrote: Dear users, How do I restart a gromacs simulation? Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 ___ 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 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 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 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 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] Re:isotropic force constant
Thank you for your advice,I have find define=-DPOSRE in my pr.mdp file, but I don't know which parameter indicate isotropic force constant of 100kjmol-1A-1. Though I use ref_t=300 for my simulation. Dear users: I have a position restrain .mdp file need to set,I use 300K in which an isotropic force constant of 100kjmol-1A-1 is applied to all nonhydroggen protein atoms. In my pr.mdp file which parameter I should add? Thank you very much! If you use pdb2gmx, it will generate a posre.itp file which you can modify to do whatever you want (although I think the above might be the default). See the manual for details on how. Then to make it work, the .mdp file needs to have 'defines = -DPOSRE' or something similar - check manual section 7.3. Mark ___ 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
