[gmx-users] Finding centroid for a bunch of residues
Hi there, This is the question out of gromacs..but I need it urgently.. and I hope this is the only place where I can get such expert to solve my query... while trying to restrict my MDRUN for a particular site of the protein molecule I want to visualize the site and find out the centroid for the particular site.. Is there any visualization tool that can do the same .. I mean Is there any molecular visualization tool that can help in finding out the ...centroid between a group of resuidues ? With Thanks, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?
Thanks for the insights, Tsjerk. I figured it was something to do with the new algorithm; just wanted to confirm that this was the expected behavior. Indeed, trjconv is one's friend in such a case :) -Justin Tsjerk Wassenaar wrote: Hi Justin, It's indeed the case that mdrun now writes broken molecules. Has to do with the domain decomposition and processors only keeping track of 'their' atoms. Too bad, but you'll just have to keep a .tpr around to make molecules whole again afterwards. Using trjconv -nojump with a suitable reference (not necessarily a .tpr) would also do it (and simultaneously remove the jumps...). Cheers, Tsjerk On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: Hi, I've been running some simulations with Gromacs 4.0 RC2, and I've noticed something strange. In the output .gro file at the end of a run, the molecules in my system (a membrane protein) are broken, crossing periodic boundaries. This affects the lipids at the periphery of the box, in my case. Has there been some change since the previous version that mdrun is now writing broken molecules to fit everything within the unit cell? Or is this behavior unintentional? -Justin -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?
Hi Justin, It's indeed the case that mdrun now writes broken molecules. Has to do with the domain decomposition and processors only keeping track of 'their' atoms. Too bad, but you'll just have to keep a .tpr around to make molecules whole again afterwards. Using trjconv -nojump with a suitable reference (not necessarily a .tpr) would also do it (and simultaneously remove the jumps...). Cheers, Tsjerk On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > Hi, > > I've been running some simulations with Gromacs 4.0 RC2, and I've noticed > something strange. In the output .gro file at the end of a run, the > molecules in my system (a membrane protein) are broken, crossing periodic > boundaries. This affects the lipids at the periphery of the box, in my case. > > Has there been some change since the previous version that mdrun is now > writing broken molecules to fit everything within the unit cell? Or is this > behavior unintentional? > > -Justin > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] .pdb to .gro => the atoms are not conneced with VMD
Chih-Ying Lin wrote: Hi .pdb to .gro => the atoms are not conneced with VMD From "Lu Tian"=> When .pdb convert to .gro,connecting information will lost,if the distance between two atoms in .gro is too long,they won't be connected. Can Gromacs recognize that they are connected from the .gro file? When running a simulation, Gromacs recognizes bonds from the .top, which get passed to the .tpr when running grompp. There is no connectivity information in the .gro by itself. -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .pdb to .gro => the atoms are not conneced with VMD
Hi .pdb to .gro => the atoms are not conneced with VMD >From "Lu Tian"=> When .pdb convert to .gro,connecting information will lost,if the distance between two atoms in .gro is too long,they won't be connected. Can Gromacs recognize that they are connected from the .gro file? Thank you Lin ___ 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] MD => system exploding
Chih-Ying Lin wrote: HI When I run MD, my system is exploding. And, I found after minimisation, the atoms of my molecule are seperated apart. That probably suggests that whatever parameters you've applied are not correct. The overall charge of my system is +1, and I put one molecule in the gas phase to do the structure test. But, it was already exploding. What is a "structure test"? What are you trying to determine? Is it hard for a +1 charge molecule to maintain a good shape under MD simulation? Gas-phase charges involve high-energy species (ionized mass spec samples, plasma, etc.), so the answer is probably yes. What is your molecule? Is it a protein? If you're using a charged protein in a vacuum, the force field you're using may not be valid. -Justin What are the procedures to test and determine the mistakes I made? Thank you Lin Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file fullmd.tpr, VERSION 3.3.3 (single precision) Loaded with Money starting mdrun 'azoct' 10 steps,100.0 ps. Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file step 10, will finish at Sun Oct 5 06:17:20 2008 --- Program mdrun, VERSION 3.3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 5832 ] --- "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD => system exploding
HI When I run MD, my system is exploding. And, I found after minimisation, the atoms of my molecule are seperated apart. The overall charge of my system is +1, and I put one molecule in the gas phase to do the structure test. But, it was already exploding. Is it hard for a +1 charge molecule to maintain a good shape under MD simulation? What are the procedures to test and determine the mistakes I made? Thank you Lin Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file fullmd.tpr, VERSION 3.3.3 (single precision) Loaded with Money starting mdrun 'azoct' 10 steps,100.0 ps. Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file step 10, will finish at Sun Oct 5 06:17:20 2008 --- Program mdrun, VERSION 3.3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 5832 ] --- "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?
Hi, I've been running some simulations with Gromacs 4.0 RC2, and I've noticed something strange. In the output .gro file at the end of a run, the molecules in my system (a membrane protein) are broken, crossing periodic boundaries. This affects the lipids at the periphery of the box, in my case. Has there been some change since the previous version that mdrun is now writing broken molecules to fit everything within the unit cell? Or is this behavior unintentional? -Justin -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PR after minimisation and PR of missing residues?
minnale wrote: Hi all, I have two doubts on PR, may be these are trivial to you. 1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps are (a)Energy minimisation (b)Position restrain with force constant descendant manner and finally (c)production. Here my doubt that, is it require to do energy minimisation between PR and production? because after PR the system equilibrating properly if do one minimisation the structure looses bad contacts with low energy, am I right? There is no need to run EM after PR. EM simply gives the system a reasonable starting point, energetically speaking. 2.If my desire protein contain some missing residues(from PDB)rectified those residues by using INSIGHT-II. Later start simulations particularly at PR, is it require to keep restrain specifically on added missing residues or whole protein residues in .itp file? I don't see any reason not to restrain the entire protein, as long as it is intact. -Justin Any suggestions would be appreciated Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Pull.pdo Columns
Hello, I understand this topic has been dealt with previously, and I have read all the relative material from the archives, but I am still having trouble deciphering what each column corresponds to in the pull.pdo file for an AFM pull, with one pull group and one reference group, and pulling in only the X direction. From what I've read, the columns are as follows: Time RefX RefY RefZ PullX PullY PullZ SpringX SpringY SpringZ ...for a total of 10 columns. The problem is that when I use the values of for the reference group and pull group at time zero to calculate end to end distance, they do not correspond to my starting pdb file after solvation. Any thoughts? __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering "You must be the change you wish to see in the world." --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .pdb to .gro => the atoms are not conneced with VMD
Hi, VMD uses a heuristic method to know if some atoms are connected. Sometimes the method fails. To be sure (and see) the atoms are well connected in VMD, you need to provided a psf file with your pdb/gro in VMD. So in your case you gro files is correct (since you indicated that your system are correct). An alternative see you gro in other software in pymol to confirm. I hope it helps Stefane -- Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com -- Message d'origine De: [EMAIL PROTECTED] de la part de [EMAIL PROTECTED] Date: dim. 05/10/2008 12:00 À: gmx-users@gromacs.org Objet : gmx-users Digest, Vol 54, Issue 18 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. PR after minimisation and PR of missing residues? (minnale ) 2. .pdb to .gro => the atoms are not conneced with VMD (Chih-Ying Lin) -- Message: 1 Date: 5 Oct 2008 05:26:52 - From: "minnale " <[EMAIL PROTECTED]> Subject: [gmx-users] PR after minimisation and PR of missing residues? To: "gmx-users1" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all, I have two doubts on PR, may be these are trivial to you. 1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps are (a)Energy minimisation (b)Position restrain with force constant descendant manner and finally (c)production. Here my doubt that, is it require to do energy minimisation between PR and production? because after PR the system equilibrating properly if do one minimisation the structure looses bad contacts with low energy, am I right? 2.If my desire protein contain some missing residues(from PDB)rectified those residues by using INSIGHT-II. Later start simulations particularly at PR, is it require to keep restrain specifically on added missing residues or whole protein residues in .itp file? Any suggestions would be appreciated Thanks in advance. -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081005/fff46f50/attachment-0001.html -- Message: 2 Date: Sun, 5 Oct 2008 01:53:36 -0700 From: "Chih-Ying Lin" <[EMAIL PROTECTED]> Subject: [gmx-users] .pdb to .gro => the atoms are not conneced with VMD To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Hi I make .pdb file to .gro file. With the VMD, the atoms are seen NOT conneced. Why? Is there any possible errors in my .gro file? Lin -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 54, Issue 18 * <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Sunil Thapa wrote: hello gmx users I am a new fellow in gromacs My structure contains 56 residues belonging to parallel helices separated by about 2 nm. I used editconf as: editconf- -bt dodecahedron -c and editconf -bt dodecahedron -d 6.5 -c where 6.5nm I used as separation of unit cells Now when I solvated using spc216. In the first case, the number of solvent molecules was more than 117000 and in the second case it was 704. Moreover, in both the cases large number of atoms lied outside the box. Can you tell me how to know the appropriate size of box for a protein structure like mine how about 1 nm (10 angstrom)? Thanks in advance Neal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
hello gmx users I am a new fellow in gromacs My structure contains 56 residues belonging to parallel helices separated by about 2 nm. I used editconf as: editconf- -bt dodecahedron -c and editconf -bt dodecahedron -d 6.5 -c where 6.5nm I used as separation of unit cells Now when I solvated using spc216. In the first case, the number of solvent molecules was more than 117000 and in the second case it was 704. Moreover, in both the cases large number of atoms lied outside the box. Can you tell me how to know the appropriate size of box for a protein structure like mine Thanks in advance Neal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
All gmx users I am a very new fellow in gromacs My structure contains 52 residues of a parallel helices with the separation of about 2 nm. I created a box with the editconf as editconf -bt dodecahedron -c ___ 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] Force constant defined in flexible TIP3P water model
Bert wrote: Dear Gromacs Users, I have a simple question about the force constants of flexible TIP3P water model defined in Gromacs. From the literature (THE JOURNAL OF CHEMICAL PHYSICS 124, 024503 2006), the force constant for bond and angle is 1059.162 kcal/mol/angstrom^2 and 68.087 kcal/mol/rad^2, which is equivalent to 443153 kJ/mol/nm^2 and 285 kJ/mol/rad^2, respectively. These two values are inconsistent with the corresponding values in tip3p.itp, which gives 502416.0 kJ/mol/nm^2 for bond and 628.02 kJ/mol/rad^2 for angle. I wanna know which one will be ok to use. Thanks for your attention. The original TIP3P model (JCP 79 (1983) 926) was rigid as far as I know. If you want a simple flexible model I would recommed TIP4P/Flex (Chem Phys Lett 372 (2003) 842). A literature search will probably reveal more models. Bert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force constant defined in flexible TIP3P water model
Dear Gromacs Users, I have a simple question about the force constants of flexible TIP3P water model defined in Gromacs. From the literature (THE JOURNAL OF CHEMICAL PHYSICS 124, 024503 2006), the force constant for bond and angle is 1059.162 kcal/mol/angstrom^2 and 68.087 kcal/mol/rad^2, which is equivalent to 443153 kJ/mol/nm^2 and 285 kJ/mol/rad^2, respectively. These two values are inconsistent with the corresponding values in tip3p.itp, which gives 502416.0 kJ/mol/nm^2 for bond and 628.02 kJ/mol/rad^2 for angle. I wanna know which one will be ok to use. Thanks for your attention. Bert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: .pdb to .gro => the atoms are not conneced with
Hi,Lin If you only loaded structure file into VMD(such as .pdb/.gro),connecting relationship will determined by distance between atoms automatically,unless the structure file have connecting information. When .pdb convert to .gro,connecting information will lost,if the distance between two atoms in .gro is too long,they won't be connected.If you want to connect them,you can use "setbonds" command in console(see VMD ug),or choose "DynamicBonds" in Drawing Method and set "Distance Cutoff" larger. Of course,don't forget to check .gro file carefully before. Lu Tian Hi I make .pdb file to .gro file. With the VMD, the atoms are seen NOT conneced. Why? Is there any possible errors in my .gro file? Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .pdb to .gro => the atoms are not conneced with VMD
Hi I make .pdb file to .gro file. With the VMD, the atoms are seen NOT conneced. Why? Is there any possible errors in my .gro file? Lin ___ 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
