[gmx-users] order parameters of partially unsaturated chains
Dear all
I wonder which is the best way to determine the deuterium order
parameters of partially unsaturated chains like the oleoyl chain of
POPC, more specifically I wonder if I should use the -unsat flag in
g_order for this case. I checked several papers on unsaturated lipids,
see for instance:
1.- http://persweb.wabash.edu/facstaff/FELLERS/publications/jpc_01.pdf
2.-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1225825/pdf/biophysj00084-0102.pdf
3.-
http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B94RW-4V8X9MG-P-1&_cdi=56421&_user=10&_pii=S0006349597782596&_coverDate=11%2F30%2F1997&_sk=%23TOC%2356421%231997%23999269994%23800076%23FLP%23display%23Volume_73,_Issue_5,_Pages_2249-2849_%28November_1997%29%23tagged%23Volume%23first%3D73%23Issue%23first%3D5%23date%23%28November_1997%29%23&view=c&_gw=y&wchp=dGLbVlz-zSkzV&md5=778ad27c9fc1e0b3874b178e36451cb4&ie=/sdarticle.pdf
4.- http://pubs.acs.org/doi/abs/10.1021/ja903529f
5.- http://www.ibpc.fr/UMR7099/pdf/Warschawski05-1.pdf
but it seems that nobody mentions anything about a correction for the
unsaturated carbons. Then I went to the code, I think this is the
important part:
if (bUnsat) {
/* Using convention for unsaturated carbons */
/* first get Sz, the vector from Cn to Cn+1 */
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], dist);
length = norm(dist);
check_length(length, a[index[i]+j], a[index[i+1]+j]);
svmul(1/length, dist, Sz);
/* this is actually the cosine of the angle between the double bond
and axis, because Sz is normalized and the two other components of
the axis on the bilayer are zero */
sdbangle += acos(Sz[axis]);
} else {
/* get vector dist(Cn-1,Cn+1) for tail atoms */
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i-1]+j]], dist);
length = norm(dist); /* determine distance between two atoms */
check_length(length, a[index[i-1]+j], a[index[i+1]+j]);
svmul(1/length, dist, Sz);
/* Sz is now the molecular axis Sz, normalized and all that */
}
As far as I see the difference is that by using the -unsat option, the
atoms Cn, Cn+1 are used to measure theta instead of the atoms Cn-1, Cn
+1. I think this could be reasonable when the whole chain is unsaturated
but I am not sure that it is correct to use the -unsat option when we
have two unsat carbons in the middle of a larger chain The
calculation could also be done for the whole chain without the -unsat
option, then repeat it for the unsaturated carbons plus their first
neighbors with the -unsat option and then replace the results obtained
from the second calculation for the central carbons in the curve
obtained without the -unsat option... as previously suggested in this
list (see
http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html)
but I am not sure that is the best... I would appreciate any comment.
Cheers,
Ángel.
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[gmx-users] error in ffgmxbon.itp
Dear Justin I want to run a simulation on a system containing DPPC and water(TIP4P-2005). I have in my .top file some included .itp files. they are: lipid.itp dppc.itp tip4p-2005.itp ffgmx-local.itp (this is the name which we have selected for the modified version of ffgmx.itp) in which they are two included files: ffgmxbon-local.itp & ffgmxnb-local.itp I have simulated this system at 310 K without error before. Now I only changed the temp to 270 K in the run.mdp file, now using the grompp command I get this error:(I sent you the command line and the error, below) I do not now what is ffdum.itp (you can see error line below) you can see below also the part of ffgmx-local.itp which the error is about that part. please let me know how to fix the error. thanks for your time -bash-3.2$ grompp_mpi -c confout-310-500.gro -f run.mdp -n index.ndx -p topoldppc.top -o topol.tpr -np 8 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -f run.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c confout-310-500.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p topoldppc.top Input Topology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 8 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling cpp... In file included from ffgmx-local.itp:9, from topoldppc.top:3: ffgmxbon-local.itp:125:22: error: ff_dum.itp: No such file or directory cpp exit code: 256 Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top > gromppAjujan' The 'cpp' command is defined in the .mdp file processing topology... ERROR 1 [file "ffgmxbon-local.itp", line 129]: Not enough parameters ERROR 2 [file "ffgmxbon-local.itp", line 130]: Not enough parameters ERROR 3 [file "ffgmxbon-local.itp", line 131]: Not enough parameters ERROR 4 [file "ffgmxbon-local.itp", line 132]: Not enough parameters ERROR 5 [file "ffgmxbon-local.itp", line 133]: Not enough parameters ERROR 6 [file "ffgmxbon-local.itp", line 134]: Not enough parameters ERROR 7 [file "ffgmxbon-local.itp", line 136]: Not enough parameters ERROR 8 [file "ffgmxbon-local.itp", line 137]: Not enou
Re: [gmx-users] error in ffgmxbon.itp
On 8/01/2011 8:44 PM, delara aghaie wrote: Dear Justin I want to run a simulation on a system containing DPPC and water(TIP4P-2005). I have in my .top file some included .itp files. they are: lipid.itp dppc.itp tip4p-2005.itp ffgmx-local.itp *(this is the name which we have selected for the modified version of ffgmx.itp)* *in which they are two included files:* ffgmxbon-local.itp *&* ffgmxnb-local.itp ** I have simulated this system at 310 K without error before. Now I only changed the temp to *270 K* in the run.mdp file, now using the grompp command I get this error:(I*sent you the command line and the error, below*) I do not now what is *ffdum.itp* (you can see error line below) you can see below also the part of *ffgmx-local.itp* which the error is about that part. please let me know how to fix the error. thanks for your time -bash-3.2$ *grompp_mpi -c confout-310-500.gro -f run.mdp -n index.ndx -p topoldppc.top -o topol.tpr -np 8 * :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION *3.3* (-: That's prehistoric. I hope you have a sufficient reason to need to use a version of GROMACS that predates your water model... Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.orgfor more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -frun.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c confout-310-500.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p topoldppc.top InputTopology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 8 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarnint 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling *cpp*... In file included from *ffgmx-local.itp*:9, from *topoldppc.top*:3: *ffgmxbon-local.itp:*125:22: error*: ff_dum.itp: No such file or directory * What's going on here? cpp exit code: 256 Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top > gromppAjujan' The 'cpp' command is defined in the .mdp file processing topology... *ERROR 1 [file "ffgmxbon-local.itp", line 129]: Not enough parameters *ERROR 2 [file "ffgmxbon-local.itp", line 130]: Not enough parameters ERROR 3 [file "ffgmxbon-local.itp", line 131]: Not enough parameters ERROR 4 [file "ffgmxbon-local.itp", line 132]: Not enough parameters ERROR 5 [file "ffgmxbo
Re: [gmx-users] Ion-Clustering?
Clustering of ions has been seen before. It is for instance discussed in Hess, B. et. al. J. Chem. Phys. 124, 164509 (2006). Cheers, Erik Micholas Smith skrev 2011-01-07 14.56: Hello everyone, I've been performing some rather long simulations (400ns) of a short peptide chain in explicit TIP4P water solvent using opls-aa forcefield with ionic concentrations near 1M, and I am finding a lot of "clustering" of my ionic species. Has anyone else run into this type of problem? I am running NPT with a temperature of 283K with berendsen coupling. For electrostatics iI am using PME, which I have been told works welll with ions in solution. The clustering of the ions reminds me of a crystallization process, this just doesn't feel like it's physical. Thanks in advance. Micholas D. Smith Graduate Student Drexel University -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
