Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? If you want to place several identical solutes with genbox -ci, then you could copy the file vdwradii.dat to the present directory and largely increase the respective vdw radii in that file (e.g. the carbon radii) before running genbox. Best, Jochen Thanks for helping! Rasoul -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] Re: slow speed
On Apr 16, 2010, at 1:40 AM, Shuangxing Dai wrote: I am not running in parallel. Right now I just changed links order from 12 to 4. It is still slow. While I change to shift, not Ewald, it finished 1 steps in 10 mins. In the paper: J Comput Chem. 2005 Dec;26(16):1701-18. GROMACS: fast, flexible, and free. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. The performance there is around 1 ps/day. I do not understand why my speed is so slow and it seems that Ewald option makes it slow. Hi, why don't you use PME then? It can also be used in parallel. Ewald is not optimized for speed. Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] manual eq. 4.74-4.75 (dihedral restraints) head scratcher
Date: Sat, 17 Apr 2010 14:58:22 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] manual eq. 4.74-4.75 (dihedral restraints) head
scratcher
Daniel L. Ensign wrote:
Hello gmx-users, you rock and rollers,
Equations 4.74 and 4.75 in my copy of the manual have (please pardon my
pseudo-LaTeX):
(4.74)
\phi' = (\phi - \phi_0) MOD 2\pi
(4.75)
V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi'
\Delta \phi
or
V(\phi') = 0 if \phi' \leq \Delta \phi
but should there be absolute values around all of the \phi-\phi_0? Which
way is it in the code -- with the absolute distance between \phi and
\phi_0 or the directed distance?
It looks like absolute values are considered. From src/gmxlib/dihres.c:
/* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
* force changes if we just apply a normal harmonic.
* Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
* This means we will never have the periodicity problem, unless
* the dihedral is Pi away from phiO, which is very unlikely due to
* the potential.
*/
dp = phi-phi0;
if (fabs(dp) dphi) {
/* dp cannot be outside (-2*pi,2*pi) */
if (dp = M_PI)
dp -= 2*M_PI;
else if(dp -M_PI)
dp += 2*M_PI;
Also, as far as I can tell (and some mornings I definitely don't read
too good) neither the manual nor
http://wiki.gromacs.org/index.php/Dihedral_Restraints define the fields
in [ dihedral_restraints ], although the latter does name them. There, I
see
[ dihedral_restraints ]
; ai ajakal type label phi dphi kfac power
57 915 1 1 180 0 1 2
ai, aj, ak, al = atom numbers, obviously
type = ?, but I'm guessing there's only one type anyway
Probably so.
label = what is this one?
Looks to be bookkeeping. The code doesn't seem to use it other than to print
debug information, but I could be wrong since I haven't surfed around it very
long.
power and label have been copied from distance restraints, but not used at all.
I have already removed them for the next release.
Berk
phi means phi0 ?
Yes.
dphi means Delta phi, I guess
Yes.
kfac is the force constant, probably
Indirectly. This term is equivalent to the fac value in distance restraints.
Since the force constant is specified in the .mdp file, different restraints
would otherwise have to be restrained with equivalent force constants. The
value of kfac is multiplied by the value of dihre_fc in the .mdp file, so
that
different restraints could have different force constants.
power = what is this one? Does 2 give me harmonic constraints?
Not a clue on this one. Also doesn't seem to be used in the code, but maybe
it's somewhere outside of dihres.c.
I'd be happy to translate any answers given to the wiki, assuming I get
answered and that I'm allowed to edit the wiki.
The wiki link you posted above doesn't actually exist any more, and actually
points to an empty page, even though the content is still online:
http://www.gromacs.org/index.php?title=Documentation/How-tos/Dihedral_Restraints
The old wiki doesn't actually exist, but has been merged into the Gromacs
site,
so if you register as a user you can make contributions. If you have
troubles,
I might get around to updating this page with the above information, unless
there is more information to be considered, or I'm wrong :)
-Justin
May the Force be with you (as long as it's calculated in hand-tuned
assembly loops),
Dan
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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[gmx-users] output of dssp
Hi, I used do_dssp_d to analyze my data. The commend was written in this way: do_dssp_d -f a.gro -s a.tpr -n a.ndx -sc dssp.xvg There are three output, #ddXB2RJu.1#, ss.xpm and dssp.xvg, be generated. What is the first output file? It is generated automatically but with nothing inside. And in my analysis I only need xvg file. How can I do to get xvg output without the others accompanied? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] output of dssp
Hsin-Lin wrote: Hi, I used do_dssp_d to analyze my data. The commend was written in this way: do_dssp_d -f a.gro -s a.tpr -n a.ndx -sc dssp.xvg There are three output, #ddXB2RJu.1#, ss.xpm and dssp.xvg, be generated. What is the first output file? A backup file of one of the intermediates in the calculation. It is unimportant. It is generated automatically but with nothing inside. And in my analysis I only need xvg file. How can I do to get xvg output without the others accompanied? You can't. The ss.xpm file is a default output file, as is the .xvg file. If you don't need it, just delete it. It's not like it would save any time to not write it out, the calculations are simply very slow for the DSSP algorithm. -Justin Hsin-Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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] CG-MD simulation of protein, always crash with protein
On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori m.j.louhivu...@rug.nlwrote: On 15 Apr 2010, at 18:06, Trang wrote: My target system is a protein with lipid molecules added randomly (using GENBOX). Running MD, I expect to I hope you're using a larger van der Waals distance (0.24nm or so) when inserting the lipids. I tried 0.3 - 0.5. It looked fine, but didn't work. broke down the problem, that is, to run md simulation for the protein molecule only, and in vacuum. Still no improvement. Although all the distances in the minimized structure are visually proper, the system exploded. If you can't run the protein even in vacuum, then the problem is either in your MD parameters, starting co-ordinates or some simple mistake somewhere. Since the .mdp files you posted seem ok, my bet is on the starting co-ordinates, just as Xavier proposed. Could you post the system topology (.top) and the protein topology (.itp), so we can rule out any mistakes in those? The protein topo is too large, so I put it here. http://pastie.org/926617 Here is the system topology. #include ../martini_v2.1.itp #include ../martini_v2.1_aminoacids.itp #include 11BHSD1.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] 11BHSD1 [ molecules ] 11BHSD1 1 You should also double check whether you have close contacts between some atoms in the protein; e.g. in VMD this is easily done using the dynamic bonds representation. -martti- Minimized structure showed no close contact (with distance cutoff 1.6, even to 1.9). Production run stopped at step 175552 (5266.56 ps) with Segmentation fault, preceeded with a lot of Lincs warnings (I set ring_bonds = constraints). This is the mdp file, this file goes along with the system in vaccuum that crashed. I'm not sure if too long simulation time can be the cause. The strange thing is that the system seemed to be relatively stable at the time of crash. rmds.xvg is below, in case you want to see the graph first-hand. -MD--- integrator = md tinit= 0.0 dt = 0.030 nsteps = 90 nstcomm = 1 comm-grps= nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 2000 nstenergy= 2000 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = nstlist = 10 ns_type = grid pbc = xyz rlist= 1.2 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = Berendsen tc-grps = Protein tau_t= 0.3 ref_t= 323 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 3.0 compressibility = 3e-5 ref_p= 1.0 gen_vel = no gen_temp = 323 gen_seed = 666 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 -- -rmsd.xvg--- @title RMSD @xaxis label Time (ps) @yaxis label RMSD (nm) @TYPE xy @ subtitle Protein after lsq fit to Protein 0.0000.0001400 150.0000.6150032 300.0000.6162945 450.0000.6451609 600.0000.6317724 750.0000.6501579 900.0000.6642945 1050.0000.6742513 1200.0000.6651280 1350.0000.6965100 1500.0000.6856629 1650.0000.7271055 1800.0000.7174531 1950.0000.7088170 2100.0000.7492073 2250.0000.7352809 2400.0000.7196461 2550.0000.7162255 2700.0000.7277457 2850.0000.7121301 3000.0000.7084662 3150.0000.7153199 3300.0000.7209989 3450.0000.7342823 3600.0000.7297466 3750.0000.7254455 3900.0000.7175814 4050.0000.7134616 4200.0000.7212958 4350.0000.7258847 4500.0000.7201833 4650.0000.7286560 4800.0000.7188574 4950.0000.715 5100.0000.7247230 5250.0000.7153631 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
