Re: [gmx-users] REMD As A Function of Distance Between 2 Chains
plz stop mailing me. - Original Message From: Huey Ling Tan [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 14 November, 2007 11:23:01 PM Subject: Re: [gmx-users] REMD As A Function of Distance Between 2 Chains Dear all , thank you for those comments, we are aware of the paper. However, we are not sure how to implement the replica exchange in gromacs. We would like to run a set of replicas in which each replica corresponds to a different set of umbrella parameters. However, when setting up a replica exchange run, all .tpr files use the same .ppa file so that each replica will have the same umbrella potential parameters. Do you know how to get around this problem. Thank you in advance, Huey Ling On 13/11/2007, Marcus Kubitzki [EMAIL PROTECTED] wrote: Hi Huey Ling, have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for details on Hamiltonian REMD, especially the correct exchange criterion. In their paper, they discuss in detail what you want to do, namely Replica Exchange Umbrella Sampling. Marcus Huey Ling Tan wrote: Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? If anyone know how this can be done? Many thanks. -- Best regards, Huey Ling ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- Best regards, Huey Ling -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about md simulation
Hi Amrita, I have faced similar problem.before MD run, try to minimize water box and protein seperately with both CG and SD, then put protein in the water box and minimize it again .., then go for MD run, I think after that you dont have any Lincs warning.. Chiradip --- amri ta [EMAIL PROTECTED] wrote: Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: Initializing LINear Constraint Solver number of constraints is 2365 average number of constraints coupled to one constraint is 2.5 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.336565 691 696 0.033770 After LINCS 0.342830698 700 0.028042 Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.858278 (between atoms 3397 and 3398) rms 0.016634 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step -1 Grid: 10 x 10 x 10 cells Configuring nonbonded kernels Testing x86_64 SSE supports...presents Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 70.089874 1537 1456 0.559021 After LINCS 29.983810 3223 3224 0.787549 Like this, errors showed Constraint error in algorithm Lincs at step 0, step1 and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this? Your advice is appreciated. Best regards, Amrita Ghosh National Institute of Mental Health and Neurosciences, Bangalore-29. India. 5, 50, 500, 5000 - Store N number of mails in your inbox. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Chiradip Chatterjee Senior research fellow Structural Biology Division Department of Biological Science National University of Singapore Phone:65-92301295 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ I LOVE KOLKATA ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] continuation of simulation
use tpbconv -h...u will find the answer... chiradip --- Michal Walczak [EMAIL PROTECTED] wrote: Hello everyone! Can anyone tell me how to carry on protein md simulation using as an input previous trajectory file, please? I mean that I've done one simulation that lasted 100 ps and now I'd like to continue it for another 100 ps starting from last step of previous simulation. Which command does it - I think reply to this question would be entirely sufficient to me. Best regards, Michal Walczak ___ 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 Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ New Yahoo! Mail is the ultimate force in competitive emailing. Find out more at the Yahoo! Mail Championships. Plus: play games and win prizes. http://uk.rd.yahoo.com/evt=44106/*http://mail.yahoo.net/uk ___ 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] [Fwd: TFE 33%]
Hi Specify exact number of TFE and Water present in your *.pdb file to *.top file..also specify *.itp of TFE in the top file... Chiradip --- Mark Abraham [EMAIL PROTECTED] wrote: i've been dealing with a simple simulation using a TFE SPC for my solvent box but i stopped every time at the (steep or em.mdp) stuff all the time. It send me this message: number of coordinates in coordinate file does not match topology ( .pdb, top 0) what should i do to over this step? do i need to change .top file whith something? or the error backs to the steep or em.mdp stuff? Thanks Please describe your problem fully... at the (steep or em.mdp) stuff doesn't help anybody work out your problem, and makes them not want to help you. When you want free help, you have to work at making it easy for someone to give it to you. If you're paying them, then do whatever you like :-) Nonetheless, it is clear that you have made an error with the formatting of your .top file. Read chapter 5 carefully and then see where your .top file doesn't satisfy the format described. Alternatively, start again with a .top file that does work for just water, and work in the TFE again. 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 Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ Inbox full of unwanted email? Get leading protection and 1GB storage with All New Yahoo! Mail. http://uk.docs.yahoo.com/nowyoucan.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
[gmx-users] g_rdf more than 8 graph edges
Hi all I encounter a Fatal error: More than 8 graph edges per atom when using g_rdf on a trajectory that was generated using 'pbc=full'. pbc=full circumvents this problem in mdrun. I have seen one entry regarding this on may 2006 and unsolved. Is there any news regarding this? thanks Chiradip Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ New Yahoo! Mail is the ultimate force in competitive emailing. Find out more at the Yahoo! Mail Championships. Plus: play games and win prizes. http://uk.rd.yahoo.com/evt=44106/*http://mail.yahoo.net/uk ___ 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] g_rdf more than 8 graph edges
Hi all I encounter a Fatal error: More than 8 graph edges per atom when using g_rdf on a trajectory that was generated using 'pbc=full'. pbc=full circumvents this problem in mdrun. I have seen one entry regarding this on may 2006 and unsolved. Is there any news regarding this? thanks Chiradip Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ New Yahoo! Mail is the ultimate force in competitive emailing. Find out more at the Yahoo! Mail Championships. Plus: play games and win prizes. http://uk.rd.yahoo.com/evt=44106/*http://mail.yahoo.net/uk ___ 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] TFE solvent box
I think replace HO by OA chiradip --- [EMAIL PROTECTED] wrote: Hi all, We want to create and simulate a solvent box containing TFE. We have already generated the TFE.gro file, and by using this file we created a box containing 38 molecules of TFE (TFE_solv.gro). We created a file TFE.top including the tfe topology (using tfe.itp, provided by GROMACS). When we executed the grompp command to generate the .tpr file, there was an error. It was shown the message below: - Fatal error: Atom type 'HO' not found ! - Can anyone tell me how to solve this problem ? Thanks a lot ! Fernando ___ 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 Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA Send instant messages to your online friends http://uk.messenger.yahoo.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
Re: [gmx-users] Dipolar correlation function
Hi David Thanks for your reply. I want to calculate dipolar corelation function C(t) between proton and fluorine using the equation: C(t) = 1/4#61552;#931;[(3cos2#952;(0)-1 )(3cos2#952;(t)-1 )]/r(0)r3(t) (ref Fellar et al, JACS 121, 8963-64, 1999) where I have a proton i and total n fluorines. At time = 0, a proton-fluorine vector has a length r(0) and is oriented at an angle #952;(0) relative to the z-axis. At a time t later in the trajectory the vector has length r(t) and is oriented at an angle #952;(t) relative to the z-axis. Is there any way to get the plot of the average C(t) vs time (ps)? Thanks in advance Chiradip --- David van der Spoel [EMAIL PROTECTED] wrote: chiradip chatterjee wrote: Hi gmx user, Is there any way in gromacs to compute dipolar correlation function between solvent atom and one atom of my protein from trajectory data? I went through g_rotacf with -d option. But I think it gives rotational correlation function for linear molecules by specifying two atoms (i,j) in the index file that means two atoms i-j with a bond. Is g_dipole -corr is an option? please advice me. Chiradip Please be more specific, what do you want to compute? Please give an equation. g_dipoles -corr computes a dipole vector from given atoms (e.g. a water molecule) and computes it's rotational autocorrelation. g_rotacf may do what you need, you don't need a bond, just a vector between two atoms. However, if they diffuse apart more than half a box periodic boundary conditions will kick in and give strange results... -- 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 Send instant messages to your online friends http://uk.messenger.yahoo.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
Re: [gmx-users] number of solvent molecule
Hi Erik I went through the documentation of g_hbond, But I think it does not give me the number of solvent molecules present in a solvent shell arround my protein. I am able to calculate no. of contacts between protein and solvent but that is not equal to the no of molecule present. Is there any suggetion? regards Chiradip --- Erik Marklund [EMAIL PROTECTED] wrote: Come to think of it, you can even skip the -contact flag if you feel like it. In any case, g_hbond is probably the way to go. Have a look at its documentation. /Erik On Tue, 2006-11-28 at 09:43 +0100, Erik Marklund wrote: g_hbond -contact. But then again, that's my answer to everything :-) Oh, and use (one of) the latest versions of gromacs, otherwise the -contact option might not work properly. /Erik On Mon, 2006-11-27 at 21:14 +, chiradip chatterjee wrote: Hi gmxusers, I am a new user of gromacs. I completed a MD run of my protein in a solvent box. Now I want to calculate the number of solvent molecules (molecules/cc) present arround a shell of 0.6nm from my protein (or sidechains). Please help me. Thanks in advance Chiradip Chatterjee Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA Send instant messages to your online friends http://uk.messenger.yahoo.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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, 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] ___ 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 Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA Send instant messages to your online friends http://uk.messenger.yahoo.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
Re: [gmx-users] number of solvent molecule
Hi Chris. thanks for ur reply. But could you please tell me the command to integrate the rdf to first maximum. I searched for it and did not find any thing and why I double the value?. Chiradip --- [EMAIL PROTECTED] wrote: I went through the documentation of g_hbond, But I think it does not give me the number of solvent molecules present in a solvent shell arround my protein. I am able to calculate no. of contacts between protein and solvent but that is not equal to the no of molecule present. Is there any suggetion? regards Chiradip Use g_rdf and integrate the radial distribution function to either a)the first minimum b)the first maximum and double the value c)some predetermined cutoff value (like 0.6nm, athough that sounds a little large to be a single solvation shell). Come to think of it, you can even skip the -contact flag if you feel like it. In any case, g_hbond is probably the way to go. Have a look at its documentation. /Erik On Tue, 2006-11-28 at 09:43 +0100, Erik Marklund wrote: g_hbond -contact. But then again, that's my answer to everything :-) Oh, and use (one of) the latest versions of gromacs, otherwise the -contact option might not work properly. /Erik On Mon, 2006-11-27 at 21:14 +, chiradip chatterjee wrote: Hi gmxusers, I am a new user of gromacs. I completed a MD run of my protein in a solvent box. Now I want to calculate the number of solvent molecules (molecules/cc) present arround a shell of 0.6nm from my protein (or sidechains). ___ 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 Send instant messages to your online friends http://uk.messenger.yahoo.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] number of solvent molecule
Hi gmxusers, I am a new user of gromacs. I completed a MD run of my protein in a solvent box. Now I want to calculate the number of solvent molecules (molecules/cc) present arround a shell of 0.6nm from my protein (or sidechains). Please help me. Thanks in advance Chiradip Chatterjee Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA Send instant messages to your online friends http://uk.messenger.yahoo.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
Re: [gmx-users] Re: Re: How to generate GRO and TOP file for
Thanks Mohan and others thanks a lot..this things help me a lot... chiradip --- Mohan Boggara [EMAIL PROTECTED] wrote: Thanks Mark, I tried atleast PRODRG, but it has the limitation on total number of atoms. Anyway, I will probably try to find a source of other packages for molecue building. Mohan On 12/11/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: How to generate GRO and TOP file for (Mark Abraham) 2. query (chiradip chatterjee) 3. Re: g_density for a micelle (Tsjerk Wassenaar) 4. Re: query (Tsjerk Wassenaar) 5. Re: query (Paul van Maaren) -- Message: 1 Date: Sun, 12 Nov 2006 08:49:16 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: How to generate GRO and TOP file for To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mohan Boggara wrote: However, to extend the gro file, we need to use the angle information and may be write a script. Molecule builders in various chemistry packages may be of help here. You may need to use a text editor to change atom and residue names in the resulting structure files (presumably PDB) but it might be better than writing your own script. I don't know if this a good idea?? A good idea is not to quote an entire daily digest when you intend only to refer to a small part of it. That digest gets sent to hundreds of people through dozens of computers each... Well done for changing the subject line to something relevant, though :-) Mark -- Message: 2 Date: Sun, 12 Nov 2006 04:45:29 + (GMT) From: chiradip chatterjee [EMAIL PROTECTED] Subject: [gmx-users] query To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi gromacs users, I am a new user in Gromacs. I need a help. I want to make a solvent box with Trifluoroethanol(TFE) and water. Could any one please supply me the *.gro and *.itp file for trifluoroethanol? I did not find this(TFE) in the library file. thanks in advance Chiradip Chatterjee Send instant messages to your online friends http://uk.messenger.yahoo.com -- Message: 3 Date: Sun, 12 Nov 2006 10:32:37 +0100 From: Tsjerk Wassenaar [EMAIL PROTECTED] Subject: Re: [gmx-users] g_density for a micelle To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Chris, Aren't you looking for a radial distribution function (g_rdf)? Maybe you'll have to change the code a bit to get exactly what you want, but I'd guess that g_rdf is closer to what you want. However, you do not state what it is you want.., so it's merely a guess. Best, Tsjerk On 11/10/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Does anybody have a modified g_density for calculation from the center of mass of a micelle? Thanks. ___ 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. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Message: 4 Date: Sun, 12 Nov 2006 10:42:42 +0100 From: Tsjerk Wassenaar [EMAIL PROTECTED] Subject: Re: [gmx-users] query To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Chiradip, Probably someone will have a topology and a structure file for TFE lying around (not me). But TFE isn't the worst of molecules and since your new with Gromacs, I think it would be an excellent opportunity to get acquinted with the program and force fields by parameterizing it yourself. Find the paper of your favorite force field (choose one) and check how the parameterization
[gmx-users] Re: query
HI friends Thanks for your instant help. I got TFE (trifluoroethanol) itp, pdb and gro files. Now I want to disturb you again for a command. I have one TFE molecule. I want to make a solvent box with 100 TFE and 600 Water molecules. What are the commands to translate this one TFE to 100TFE in a mixed solvent box? [I found the water box filled with water in share/tutor/water.] Sorry to bother you, But it seems to be that you guys are my teachers of GROMACS as I am just a 4 days old baby in gromacs. Chiradip --- David van der Spoel [EMAIL PROTECTED] wrote: Paul van Maaren wrote: On Sunday 12 November 2006 10:42, Tsjerk Wassenaar wrote: Probably someone will have a topology and a structure file for TFE lying around (not me). But TFE isn't the worst of molecules and since your new with Gromacs, I think it would be an excellent opportunity to get acquinted with the program and force fields by parameterizing it yourself. Find the paper of your favorite force field (choose one) and check how the parameterization of the building blocks / molecules was done. Take the same steps for TFE. Maybe this isn't the answer you'd hoped for, but think of the saying give a man a fish and he can eat for a day; teach a man how to fish and... :) That's always a good approach, but for starters you might want to take a look at tfe.itp in the share/top directory. ... and check recent literature. IIRC there is a quite recent TFE model for GROMOS-like force fields. -- 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 Send instant messages to your online friends http://uk.messenger.yahoo.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
