Re: [gmx-users] Genbox problem with TIP4P water with OPLS
On Thu, Feb 19, 2009 at 01:56:28AM +1100, Mark Abraham wrote: > Chao Zhang wrote: > >Hi Mark, > > > >I think 3.3.2, does it be fixed in 4.0? > > I don't know - I've not seen it reported. You should search the mailing > list archives. I've solvated with tip4p in 3.3cvs and 3.3.1, never had the problem. anyway, a `grep 'OW SOL' box.pdb | wc -l` will tell you how many solvent molecules you have. cheers, marc ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox problem with TIP4P water with OPLS
Chao Zhang wrote: Hi Mark, I think 3.3.2, does it be fixed in 4.0? I don't know - I've not seen it reported. You should search the mailing list archives. There won't be any interest in diagnosing or fixing it within version 3.x, but if you can reproduce your result in 4.0.4, file a bugzilla from the GROMACS website and it'll get attention. Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox problem with TIP4P water with OPLS
Hi Mark, I think 3.3.2, does it be fixed in 4.0? Chao On Wed, Feb 18, 2009 at 12:06 PM, Mark Abraham wrote: > Chao Zhang wrote: > >> Dear gmx-user, >> >> I try to build a pure water box in Gromacs, so I just solved one water as >> solute with genbox. >> >> When I use tip3p water, my scripts work well. But to switch to tip4p >> water, there seems a bug, I don't know whether people have noticed this or >> not. >> >> The system shows that it added 350 water but just write 349 water in >> topology file, therefore failed the test of grompp. Any suggestion? >> >> # >> Added 350 molecules >> Generated solvent containing 1400 atoms in 350 residues >> Writing generated configuration to test_sol.gro >> >> Back Off! I just backed up test_sol.gro to ./#test_sol.gro.5# >> salt in water >> >> Output configuration contains 1404 atoms in 351 residues >> Volume : 9.95267 (nm^3) >> Density: 1055.19 (g/l) >> Number of SOL molecules:350 >> Processing topology >> Adding line for 349 solvent molecules to topology file (test.top) >> >> > > What version of GROMACS is this? > > Mark > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Chao Zhang ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox problem with TIP4P water with OPLS
Chao Zhang wrote: Dear gmx-user, I try to build a pure water box in Gromacs, so I just solved one water as solute with genbox. When I use tip3p water, my scripts work well. But to switch to tip4p water, there seems a bug, I don't know whether people have noticed this or not. The system shows that it added 350 water but just write 349 water in topology file, therefore failed the test of grompp. Any suggestion? # Added 350 molecules Generated solvent containing 1400 atoms in 350 residues Writing generated configuration to test_sol.gro Back Off! I just backed up test_sol.gro to ./#test_sol.gro.5# salt in water Output configuration contains 1404 atoms in 351 residues Volume : 9.95267 (nm^3) Density: 1055.19 (g/l) Number of SOL molecules:350 Processing topology Adding line for 349 solvent molecules to topology file (test.top) What version of GROMACS is this? Mark ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Genbox problem with TIP4P water with OPLS
Dear gmx-user, I try to build a pure water box in Gromacs, so I just solved one water as solute with genbox. When I use tip3p water, my scripts work well. But to switch to tip4p water, there seems a bug, I don't know whether people have noticed this or not. The system shows that it added 350 water but just write 349 water in topology file, therefore failed the test of grompp. Any suggestion? # Added 350 molecules Generated solvent containing 1400 atoms in 350 residues Writing generated configuration to test_sol.gro Back Off! I just backed up test_sol.gro to ./#test_sol.gro.5# salt in water Output configuration contains 1404 atoms in 351 residues Volume : 9.95267 (nm^3) Density: 1055.19 (g/l) Number of SOL molecules:350 Processing topology Adding line for 349 solvent molecules to topology file (test.top) -- Chao Zhang ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox problem with micelle
Alif M Latif wrote: Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p Thanks 4 reading...any comments and suggestion will be greatly appreciated.. A third alternative would be to increase the vdw radii, by copying vdwradii.dat to your working directory and increase the water radius. -- 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 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] genbox problem with micelle
If you have the center coordinates and your cell has a good radial symmetry, i would just write a script, checking the distance of each water to the center and then skipping everything below the radius of your cell. Cheers Martin ___ 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] genbox problem with micelle
> Dear GROMACS users and developers.. > > I'm trying to run MD simulation on a micelle structure, which i've built > using Packmol. The problem is when i use genbox to solvate the system > using SPC water, the water came inside the micelle, and my simulation > didn't produce any significant changes to the structure (the behavior of > lipids which are lipophilic should squeezed the water molecules outside > the micelle structure). I'm wondering if i can tell genbox not to put > water molecule inside the micelle...can i?.. :-p genbox just uses vdw radii for different atom types to generate volumes that exclude waters. If your micelle (and I presume from the above that you have a micelle that is lipid-inside-surface water-outside-surface) has interstices that are large enough to admit waters, then genbox will place them there. Probably, an energy minimization of the micelle in vacuo will see it contract so that the lipids are pretty much close-packed, and hopefully this density will also be close to that for the micelle in solution. Alternatively, or if there are still holes that admit waters, you can make the radii of your lipid C and H atoms larger for the purposes of genbox using a modified gromacs/share/top/vdwradii.dat. Be careful later with the gentleness of your minimization and equilibration schemes else you'll generate large structural changes and thus bad contacts and LINCS errors, etc. Otherwise, you could get out a molecule visualization program like VMD, find the waters inside and delete them (you could script this with VMD, too). There's also a lesson here to look at your structure before you simulate to see that it looks how you expect it to. If you'd seen these waters, and knew for some reason that it would take longer than your simulation time to form an equilibrated micelle by excluding these waters, then you'd have known not to bother with this simulation, and fixed your problem without spending computer time needlessly. Mark ___ 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] genbox problem with micelle
Dear GROMACS users and developers.. I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p Thanks 4 reading...any comments and suggestion will be greatly appreciated.. Alif Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ ___ 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] Genbox problem ...
Yeah actually I got cause of the problem... :) I need to remove the "topinput" file before renaming "TEMP_FILENM" with " topinput". Thanks... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, May 29, 2007 6:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Genbox problem ... Kedar Potdar wrote: > Hi friends, > > > > I have compiled Gromacs on native windows. The first two program in demo > script (perl implementation of script "demo") work fine but genbox > displays following output > > > > Reading solute configuration > > Glycine aRginine prOline Methionine Alanine Cystine Serine > > Containing 145 atoms in 13 residues > > Initialising van der waals distances... > > Reading solvent configuration > > "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" > > solvent configuration contains 648 atoms in 216 residues > > > > Initialising van der waals distances... > > Will generate new solvent configuration of 2x2x2 boxes > > Generating configuration > > Sorting configuration > > Found 1 molecule type: > > SOL ( 3 atoms): 1728 residues > > Calculating Overlap... > > box_margin = 0.315 > > Removed 2895 atoms that were outside the box > > Succesfully made neighbourlist > > nri = 11448, nrj = 456822 > > Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms. > > Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms. > > Added 488 molecules > > Generated solvent containing 1464 atoms in 488 residues > > Writing generated configuration to cpeptide_b4em.gro > > Glycine aRginine prOline Methionine Alanine Cystine Serine > > > > Output configuration contains 1609 atoms in 501 residues > > Volume : 17.1176 (nm^3) > > Density: 1002.99 (g/l) > > Number of SOL molecules:488 > > > > Processing topology > > > > Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1# > > > > *Cpeptide.top file is of zero bytes now. and all further programs in the > test fail after this.* > > * * > > Has anybody faced such problem before? What is remedy for this problem? > Check the source code for opening of the file in genbox. It tries to append to the file, and the code for that may be different windows than under Unix. -- 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 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 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] Genbox problem ...
Kedar Potdar wrote: Hi friends, I have compiled Gromacs on native windows. The first two program in demo script (perl implementation of script “demo”) work fine but genbox displays following output Reading solute configuration Glycine aRginine prOline Methionine Alanine Cystine Serine Containing 145 atoms in 13 residues Initialising van der waals distances... Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 2895 atoms that were outside the box Succesfully made neighbourlist nri = 11448, nrj = 456822 Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms. Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms. Added 488 molecules Generated solvent containing 1464 atoms in 488 residues Writing generated configuration to cpeptide_b4em.gro Glycine aRginine prOline Methionine Alanine Cystine Serine Output configuration contains 1609 atoms in 501 residues Volume : 17.1176 (nm^3) Density: 1002.99 (g/l) Number of SOL molecules:488 Processing topology Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1# *Cpeptide.top file is of zero bytes now… and all further programs in the test fail after this.* * * Has anybody faced such problem before? What is remedy for this problem? Check the source code for opening of the file in genbox. It tries to append to the file, and the code for that may be different windows than under Unix. -- 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 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] Genbox problem ...
Hi friends, I have compiled Gromacs on native windows. The first two program in demo script (perl implementation of script "demo") work fine but genbox displays following output Reading solute configuration Glycine aRginine prOline Methionine Alanine Cystine Serine Containing 145 atoms in 13 residues Initialising van der waals distances... Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 2x2x2 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 1728 residues Calculating Overlap... box_margin = 0.315 Removed 2895 atoms that were outside the box Succesfully made neighbourlist nri = 11448, nrj = 456822 Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms. Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms. Added 488 molecules Generated solvent containing 1464 atoms in 488 residues Writing generated configuration to cpeptide_b4em.gro Glycine aRginine prOline Methionine Alanine Cystine Serine Output configuration contains 1609 atoms in 501 residues Volume : 17.1176 (nm^3) Density: 1002.99 (g/l) Number of SOL molecules:488 Processing topology Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1# Cpeptide.top file is of zero bytes now. and all further programs in the test fail after this. Has anybody faced such problem before? What is remedy for this problem? With warm regards, KEDAR ___ 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] genbox problem
Roman Holomb wrote: Dear Gromacs users, I use genbox for random insert 100 BF4 molecules in the box. But there are so many connections between BF4 anions . I have decreased number of molecules to 20 but I have the same problem. Sometimes this can be fixed by energy minimization. After optimization I have no connections between different BF4 anions but there are small amount of BF4 with F-F bonds. This is realy problem to use "genbox" for generate the model (I plan to make more complicated systems and I have no posibility to correct models "by hand" So my question is: Can I do something with parameters (VDW coulomb distance) to get correct results from genbox? Seems nothing influence here . edit vdwradii.dat Thanks Sincerely /Roman ___ 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 -- 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
[gmx-users] genbox problem
Dear Gromacs users, I use genbox for random insert 100 BF4 molecules in the box. But there are so many connections between BF4 anions . I have decreased number of molecules to 20 but I have the same problem. Sometimes this can be fixed by energy minimization. After optimization I have no connections between different BF4 anions but there are small amount of BF4 with F-F bonds. This is realy problem to use "genbox" for generate the model (I plan to make more complicated systems and I have no posibility to correct models "by hand" So my question is: Can I do something with parameters (VDW coulomb distance) to get correct results from genbox? Seems nothing influence here . Thanks Sincerely /Roman ___ 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
