[gmx-users] r.m.s.i.p
Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! ___ Mp3疯狂搜-新歌热歌高速下 http://music.yahoo.com.cn/?source=mail_mailbox_footer ___ 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] r.m.s.i.p
xi zhao wrote: > Dear Gromacs users: > I am a new gromacs user, I want ro calculate r.m.s.i.p > for exploring similar in motions of two different > proteins, I need a script or tools to calculate it. I > need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. 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
回复： Re: [gmx-users] r.m.s.i.p
Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear Gromacs users:> I am a new gromacs user, I want ro calculate r.m.s.i.p> for exploring similar in motions of two different> proteins, I need a script or tools to calculate it. I> need your help!I don't know what r.m.s.i.p is. If you want to get help, please definecarefully what you are trying to do - even a link to a journal articlemight work. Please read carefully the gromacs manual section thatdescribes what the utility programs do, in case one of them does it.Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Mp3疯狂搜-新歌热歌高速下 ___ 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: Simulation problem with extended membrane system!
Thanks Chris, I really appreciate your help!I've got my extended membrane system regarding your note, and now I'm testing it with my GPCR. I am still not very familiar with the script, I think it will take some time to learn. Thanks again!On 9/13/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote:>If I solvate my GPCR into the DPPC128 system using genbox, there are only >about 50 lipids left, which I think are too few, so I want a larger starting>structure.>According to your note, when I did step 3, loaded my DPPC183 system to VMD,>I found the edges lined up poorly, there is are gaps between two periodic >cells. I also try other system like DPPC200, DPPC150, but only the original>dppc128 system, I've equilibrated it for 2ns, have no gap between two>periodic cells.>So, I will try another starting structure, like POPC, DMPC or your POPE. But >I still can't figure out why there are gaps when using genbox to extend the>DPPC system.It's because any overlap causes an entire lipid to be removed.If you don't want to equilibrate, try exactly doubling your system size in x and y. That should work perfectly.___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww 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 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
回复： Re: [gmx-users] r.m.s.i.p
Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear Gromacs users:> I am a new gromacs user, I want ro calculate r.m.s.i.p> for exploring similar in motions of two different> proteins, I need a script or tools to calculate it. I> need your help!I don't know what r.m.s.i.p is. If you want to get help, please definecarefully what you are trying to do - even a link to a journal articlemight work. Please read carefully the gromacs manual section thatdescribes what the utility programs do, in case one of them does it.Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 雅虎免费邮箱-3.5G容量，20M附件___ 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: 回复： Re: [gmx-users] r.m.s.i.p
Hi Xi Zhao, Please find attached a .csh script you can use to calculate the rmsip. The script is of the hand of Isabella Daidone, now in Heidelberg. Note that for a set of 'equal' simulations there is a spread in the values you obtain for the RMSIP (i.e. it's not an absolute measure of equality unless you have full convergence of your simulations). If you want to use the RMSIP to really compare simulations check our paper in JCC 27 p. 316 (2006). Cheers, Tsjerk On 9/18/06, xi zhao <[EMAIL PROTECTED]> wrote: Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear Gromacs users: > I am a new gromacs user, I want ro calculate r.m.s.i.p > for exploring similar in motions of two different > proteins, I need a script or tools to calculate it. I > need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. Mark ___ gmx-users mailing list gmx-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 雅虎免费邮箱-3.5G容量，20M附件 ___ 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. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 xpm2normal.csh Description: C-Shell script ___ 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: 回复： Re: [gmx-users] r.m.s.i.p
HI Zhao, To compute RMSIP, you have to compute eigenvector using gromacs utility program then from that trajectory you can compute RMSIP using a script which I got from Tsjerk Wassenaar from this list. You can appraoch him. Regards, B.Nataraj On Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao" <[EMAIL PROTECTED]> said: > Based on the essential dynamics analysis, the similar of the internal > fluctuations in may simulation systems was evaluated by comparing > principal subspace first 10 eigenvectors) of each structural trajectory > by using the root mean square inner product(RMSIP). Amadei, A., > de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. > A kinetic model for the internal motions of proteins: diffusion between > multiple harmonic wells. Proteins. 1999. 35, 283-292. > > > Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > > Dear Gromacs users: > > I am a new gromacs user, I want ro calculate r.m.s.i.p > > for exploring similar in motions of two different > > proteins, I need a script or tools to calculate it. I > > need your help! > > I don't know what r.m.s.i.p is. If you want to get help, please define > carefully what you are trying to do - even a link to a journal article > might work. Please read carefully the gromacs manual section that > describes what the utility programs do, in case one of them does it. > > Mark > ___ > gmx-users mailing list gmx-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 > > > > - > > 雅虎免费邮箱-3.5G容量，20M附件 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? ___ 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] short range nonbondeds = 0 in power4
On Fri, 15 Sep 2006, Atte Sillanpää wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. Hi, the problem seems solved. I removed the --enable-threads from the gromacs config options and now short range forces come out right. Simulations are stable and e.g. water rdfs are identical in power4 and amd opteron. It's a little bit nasty that compiler gets through the threads flag but then computes garbage. It has been said in the mailing list that threads don't work yet, but that's hard to find as the solution unless you know to look for it. To further check my binary I'd like to do some other tests. I tried looking for the benchmarks, but the link doesn't work (search for 'bench' at the gromacs site). Are they still available (and do they have some verified results to compare to?) Thanks, Atte___ 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] short range nonbondeds = 0 in power4
Atte Sillanpää wrote: On Fri, 15 Sep 2006, Atte Sillanpää wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. Hi, the problem seems solved. I removed the --enable-threads from the gromacs config options and now short range forces come out right. Simulations are stable and e.g. water rdfs are identical in power4 and amd opteron. It's a little bit nasty that compiler gets through the threads flag but then computes garbage. It has been said in the mailing list that threads don't work yet, but that's hard to find as the solution unless you know to look for it. To further check my binary I'd like to do some other tests. I tried looking for the benchmarks, but the link doesn't work (search for 'bench' at the gromacs site). Are they still available (and do they have some verified results to compare to?) Thanks, For now you can download them using good old ftp (user anonymous pass your email) We will fix the website. Atte ___ 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
Re: [gmx-users] The molecule size
主月 ：） wrote: > Hi: > > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition . > > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too small to accept as follows. > > The Rg for PE (C1000) is just 28 angstrom. It means the infinite > charaterastic ratio (Cinf) for the polymer is just about 2 which is much > smaller than scatter experimental value about 7. > > The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for > the polymer is just 2.5 which is much smaller than scatter experimental > value 8-10. > > Can these results be accepted? > > Is there any fault in force field? gromos96a Two things, - maybe you need a larger systems - maybe g_gyrate does not take periodicity into account correctly. extract some single molecules and look at them in a viewer, or write your own script to compute Rg. - have you used pbc = full for the simulations? Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark *Hi Mark:* *Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details.* ** *The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl = no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time is about 1ns. So i think the system has been relaxed enough.* ** *Is there any error in my process?* ** *Maybe the residue parameter for PVME is also needed for discuss. They are:* ** -- 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] n-hexadecane simulation
Dear all GROMACS users: I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic angle potential, and Rychaert-Bellemans torsion model. However, it is so unstable for 2fs time step - The bond length suddenly diverges. The simulation becomes stable for 0.2 fs time step, which seems too small. Could anybody give an instruction for this problem? Followings are my .mdp and topology files. Thank you in advance for your kind instruction. ; VARIOUS PREPROCESSING OPTIONS = title= 2*2 pore cpp = /lib/cpp integrator = md dt = 0.002 nsteps = 600 nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstenergy= 1000 ;Output frequency and precision for xtc file = nstxtcout= 500 xtc_precision= 1 xtc-grps = HEX ; CONSTRAINT SCHEME constraints = all-bonds constraint_algorithm = lincs ; Selection of energy groups = energygrps = HEX ; NEIGHBORSEARCHING PARAMETERS = nstlist = 10 ns_type = grid pbc = xyz ; OPTIONS FOR WEAK COUPLING ALGORITHMS = tcoupl = nose-hoover tc-grps = HEX tau_t= 0.3 ref_t= 300.0 rcoulomb = 1.49 rlist= 1.38 rvdw = 1.38 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300.0 gen_seed = 94729 [ moleculetype ] ; molname nrexcl HEX 3 [ atoms ] ; nr type resnr residue atom cgnr charge 1CH3 1HEXC1 1 0.000 2CH2 1HEXC2 1 0.000 3CH2 1HEXC3 1 0.000 4CH2 1HEXC4 1 0.000 5CH2 1HEXC5 1 0.000 6CH2 1HEXC6 1 0.000 7CH2 1HEXC7 1 0.000 8CH2 1HEXC8 1 0.000 9CH2 1HEXC9 1 0.000 10CH2 1HEXC10 1 0.000 11CH2 1HEXC11 1 0.000 12CH2 1HEXC12 1 0.000 13CH2 1HEXC13 1 0.000 14CH2 1HEXC14 1 0.000 15CH2 1HEXC15 1 0.000 16CH3 1HEXC16 1 0.000 [ constraints ] 12 2 0.153 23 2 0.153 34 2 0.153 45 2 0.153 56 2 0.153 67 2 0.153 78 2 0.153 89 2 0.153 9 10 2 0.153 10 11 2 0.153 11 12 2 0.153 12 13 2 0.153 13 14 2 0.153 14 15 2 0.153 15 16 2 0.153
[gmx-users] Re: Simulation problem with extended membrane system!
If you use the script as I have suggested,
http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html
The script is designed for a gro file that does not have any
velocities written into it, ie. it looks like this:
1THR N1 0.801 6.473 -0.310
1THR H12 0.760 6.476 -0.402
1THR H23 0.865 6.394 -0.304
If you have 3 additional columns in your .gro file, then you need to
change the script like this:
l=${#line}
m=$(expr $l - 24) # ADD THIS LINE ONLY IF VELOCITIES ARE IN YOUR .GRO
The first line is #37 I think, and the next line is the line that you
need to add. This says "Ignore the velocities"
Also, if you use TIP4p then line 30 needs to be
if [ "$count" = 4 ]; then
instead of
if [ "$count" = 3 ]; then
Likewise, use "5" if you use tip5p.
Chris.
___
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] n-hexadecane simulation
You could change the lincs_iter. I would use SHAKE rather than LINCS. For n-alkanes using the model of Ryckaert-Bellemans, it is OK. Anyway, 2fs is correct. Jae Hyun Park wrote: Dear all GROMACS users: I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic angle potential, and Rychaert-Bellemans torsion model. However, it is so unstable for 2fs time step - The bond length suddenly diverges. The simulation becomes stable for 0.2 fs time step, which seems too small. Could anybody give an instruction for this problem? Followings are my .mdp and topology files. Thank you in advance for your kind instruction. ; VARIOUS PREPROCESSING OPTIONS = title= 2*2 pore cpp = /lib/cpp integrator = md dt = 0.002 nsteps = 600 nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstenergy= 1000 ;Output frequency and precision for xtc file = nstxtcout= 500 xtc_precision= 1 xtc-grps = HEX ; CONSTRAINT SCHEME constraints = all-bonds constraint_algorithm = lincs ; Selection of energy groups = energygrps = HEX ; NEIGHBORSEARCHING PARAMETERS = nstlist = 10 ns_type = grid pbc = xyz ; OPTIONS FOR WEAK COUPLING ALGORITHMS = tcoupl = nose-hoover tc-grps = HEX tau_t= 0.3 ref_t= 300.0 rcoulomb = 1.49 rlist= 1.38 rvdw = 1.38 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300.0 gen_seed = 94729 [ moleculetype ] ; molname nrexcl HEX 3 [ atoms ] ; nr type resnr residue atom cgnr charge 1CH3 1HEXC1 1 0.000 2CH2 1HEXC2 1 0.000 3CH2 1HEXC3 1 0.000 4CH2 1HEXC4 1 0.000 5CH2 1HEXC5 1 0.000 6CH2 1HEXC6 1 0.000 7CH2 1HEXC7 1 0.000 8CH2 1HEXC8 1 0.000 9CH2 1HEXC9 1 0.000 10CH2 1HEXC10 1 0.000 11CH2 1HEXC11 1 0.000 12CH2 1HEXC12 1 0.000 13CH2 1HEXC13 1 0.000 14CH2 1HEXC14 1 0.000 15CH2 1HEXC15 1 0.000 16CH3 1HEXC16 1 0.000 [ constraints ] 12 2 0.153 23 2 0.153 34 2 0.153 45 2 0.153 56 2 0.153 67 2 0.153 78 2 0.153 89 2 0.153 9 10 2 0.153 10 11 2 0.153 11 12 2 0.153 12 13 2 0.153 13 14 2 0.153 14
[gmx-users] re: n-hexadecane simulation
You have #2 in the 3rd column which nmeans that you are not excluding 1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change this value to a one instead of a two. That should fix your problem. However, I would recommend that you set up the regular RB bonds like this. That way you have the settings in case you want to stop constraining bond lengths. Remove your [ constraints ] section and adding this: [ bonds ] 12 1 0.15300E+00 0.33470E+06 23 1 0.15300E+00 0.33470E+06 34 1 0.15300E+00 0.33470E+06 45 1 0.15300E+00 0.33470E+06 56 1 0.15300E+00 0.33470E+06 67 1 0.15300E+00 0.33470E+06 78 1 0.15300E+00 0.33470E+06 89 1 0.15300E+00 0.33470E+06 9 10 1 0.15300E+00 0.33470E+06 10 11 1 0.15300E+00 0.33470E+06 11 12 1 0.15300E+00 0.33470E+06 12 13 1 0.15300E+00 0.33470E+06 13 14 1 0.15300E+00 0.33470E+06 14 15 1 0.15300E+00 0.33470E+06 15 16 1 0.15300E+00 0.33470E+06 Chris. ___ 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] Bonds
Hi! I have a question . I am working with a proteina that they will count two centers FES co-ordinated for cisteins, these cisteins were not on to iron atoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimização, I made one md with restricted position, when I make the total dynamic with I tie occurs error in the algorithm shake and it stops in the first steps informing that I did not obtain to set molecules of water. I am using the field of force of gromacs (option 4) and the water is spc216. ESS ___ 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] protein unstable for parallel job while stable for serial one
Hello Has anybody seen a protein becoming unstable on parallel nodes while remaining stable on single node? I am running a NPT molecular dynamics simulation. The system contains a protein with 141 residues surrounded by water making the total to 32714 atoms. I ran this simulation at two places for 8ns. One as a serial job and the other as a parallel job on 16 nodes. The protein remains stable all through for the serial job but for parallel job the protein opens up after 3ns of simulation and is never stable after that. All other conditions are exactly the same. Any help would be highly appreciated. Akansha Akansha Saxena Graduate Student Department of Biomedical Engineering Washington University in St Louis __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.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] merger ligand and protein to constriant
Try the following way: But you shoul get you top file and gro file without the ligand. Then If your protein has 100 residues, add you ligand as residue 101 in the gro file. After residue add the "TER" . In ddition, adding the ligand ITP file to the later part of the Gro file. -Original Message- From: [EMAIL PROTECTED] on behalf of ?? Sent: Tue 9/12/2006 7:07 AM To: gmx-users@gromacs.org Subject: Re:[gmx-users] merger ligand and protein to constriant What about merging the ligand the the protein by DeepView? In your mail: >From: "kanin wichapong" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] merger ligand and protein to constriant >Date:Tue, 12 Sep 2006 13:40:59 +0200 > >Hi all > I already look in the turorial however that is not the thing that I try to >look for. I would like to merge the ligand into the protein and then make >the contrain between two atoms, one from the liagand and one from the >protein. However, as far as I know, I can do the constraint or restraint >just in the one chain. I cant do that with the different chain. So that i >try to merge ligand chain and protein chain. I tried to do that with pdb2gmx >but it is not work. So that i would like to know is there any way to merge >the ligand chain with the protein chain. >Thanks for all your suggstions > >Best Regard >Kanin >___ >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 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 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] r.m.s.i.p
Try RMSD fit function. -Original Message- From: [EMAIL PROTECTED] on behalf of xi zhao Sent: Mon 9/18/2006 2:12 AM To: gmx-users@gromacs.org Subject: [gmx-users] r.m.s.i.p Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! ___ Mp3???-??? http://music.yahoo.com.cn/?source=mail_mailbox_footer ___ 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 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: n-hexadecane simulation
Thank you so much for your consideration. However, it still diverge even after correcting the number in 3rd column and using bond parameters. Also, using SHAKE is not helpful. I'm using single-precision GROMACS. Is it make this kind of problem? What else can I do try? Thank you in advance for your kind instruction. Jae Original message >Date: Mon, 18 Sep 2006 11:13:03 -0400 >From: [EMAIL PROTECTED] >Subject: [gmx-users] re: n-hexadecane simulation >To: gmx-users@gromacs.org > >You have #2 in the 3rd column which nmeans that you are not excluding >1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change >this value to a one instead of a two. That should fix your problem. >However, I would recommend that you set up the regular RB bonds like >this. That way you have the settings in case you want to stop >constraining bond lengths. > >Remove your [ constraints ] section and adding this: > >[ bonds ] > 12 1 0.15300E+00 0.33470E+06 > 23 1 0.15300E+00 0.33470E+06 > 34 1 0.15300E+00 0.33470E+06 > 45 1 0.15300E+00 0.33470E+06 > 56 1 0.15300E+00 0.33470E+06 > 67 1 0.15300E+00 0.33470E+06 > 78 1 0.15300E+00 0.33470E+06 > 89 1 0.15300E+00 0.33470E+06 > 9 10 1 0.15300E+00 0.33470E+06 >10 11 1 0.15300E+00 0.33470E+06 >11 12 1 0.15300E+00 0.33470E+06 >12 13 1 0.15300E+00 0.33470E+06 >13 14 1 0.15300E+00 0.33470E+06 >14 15 1 0.15300E+00 0.33470E+06 >15 16 1 0.15300E+00 0.33470E+06 > > >Chris. > >___ >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 === Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) [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
[gmx-users] a problem about Coul-LR in energy groups output. Coul-LR is always ZERO !
I want to analyze the energy during a normal simulation. Some strange things happened. In mdp file, I selected DNA, NA+, SOL for energy groups output. When I analyzed edr file by g_energy, I found Coul_LR is always ZERO. I think my parameters have no problem, rlist = 1.0 rcoulomb = 1.0, rvdw = 1.0. Furthermore, when I selected 'System' for energy output, Coul_LR have some reasonable values. When I do MD simulation in other computer, there is NO output for Coul-LR with the SAME parameter file. ___ 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] re: n-hexadecane simulation
1. Try the [ bonds ] section that I mentioned earlier and remove the [ constraints ] section. 2. Did you do an energy minimization? If so, what total Energy and max force do you acheive? 3. What is the size of your box? Is it >=3.0nm? Is that also larger than 1.49 + max_n-hexadecane_length? It should be both of these, although only the first issue is likely to show up as an energy error. 4. What vdwtype and coulombtype are you using? This might be problematic: rcoulomb = 1.49 rlist= 1.38 rvdw = 1.38 Try this instead: coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 ___ 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] Gromacs install question
Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configure 4. make 5 make install The result is that only the following commands are installed in /bin directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, pdb2gmx,protonate,tpbconv, x2top. What wrong with it? who can tell me? Thanks in advance! -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ 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] single point calculation
Hi, is my firt question in the list, i have a very simple and posibly a very nonsense question. do i have to use mdrun to performe a single point calculation of a certain conformation? how? is there something to specify in .mdp file? Can some body provide me an example of how to use ffscan? with a small molecule if it is possible... Best regards reynier ___ 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] bonds
Hi! I have a question . I am working with a protein that they will count twocenters FES co-ordinated for cisteins, these cisteins were not on to ironatoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimização, Imade one md with restricted position, when I make the total dynamic with Itie occurs error in the algorithm shake and it stops in the first steps informing that I did not obtain to set molecules of water. I am using thefield of force of gromacs (option 4) and the water is spc216. ESS ___ 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] velocities
Dear Gromacs Users, I am getting different results for simulations with " gen_vel=yes" and "gen_vel= no". I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200K and last 300K. (with 'gen_vel=no' for all MD) Is it correct? Because I read both 'yes' and 'no' as possibilites in some references. Iam bit confused which to use for exact simulations. Any help will be appreciated. Thanks in advance Best regards Gajula ___ 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] Gromacs install question
In your sudirectory of the newly established Gromacs directory, there will subdirectory tools and kernel. You can start your commands in these subdirectory and it should work. Best regards. Fenghui Fan -Original Message- From: [EMAIL PROTECTED] on behalf of Qiao Baofu Sent: Mon 9/18/2006 3:05 PM To: Discussion list for GROMACS users Subject: [gmx-users] Gromacs install question Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configure 4. make 5 make install The result is that only the following commands are installed in /bin directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, pdb2gmx,protonate,tpbconv, x2top. What wrong with it? who can tell me? Thanks in advance! -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ 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
回复： RE: [gmx-users] r.m.s.i.p
how to use it in detail?Thanks!"Fan, Fenghui " <[EMAIL PROTECTED]> 写道： Try RMSD fit function.-Original Message-From: [EMAIL PROTECTED] on behalf of xi zhaoSent: Mon 9/18/2006 2:12 AMTo: gmx-users@gromacs.orgSubject: [gmx-users] r.m.s.i.pDear Gromacs users:I am a new gromacs user, I want ro calculate r.m.s.i.pfor exploring similar in motions of two differentproteins, I need a script or tools to calculate it. Ineed your help!Thank you in advance!Best regard! ___ Mp3???-???http://music.yahoo.com.cn/?source=mail_mailbox_footer___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 抢注雅虎免费邮箱-3.5G容量，20M附件！ ___ 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
回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p
Dear Tsjerk : Thank you very much!Tsjerk Wassenaar <[EMAIL PROTECTED]> 写道： Hi Xi Zhao,Please find attached a .csh script you can use to calculate the rmsip.The script is of the hand of Isabella Daidone, now in Heidelberg.Note that for a set of 'equal' simulations there is a spread in thevalues you obtain for the RMSIP (i.e. it's not an absolute measure ofequality unless you have full convergence of your simulations). If youwant to use the RMSIP to really compare simulations check our paper inJCC 27 p. 316 (2006).Cheers,TsjerkOn 9/18/06, xi zhao <[EMAIL PROTECTED]>wrote:> Based on the essential dynamics analysis, the similar of the internal> fluctuations in may simulation systems was evaluated by comparing principal> subspace first 10 eigenvectors) of each structural trajectory by using the> root mean square inner product(RMSIP).> Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. &> Berendsen, H. J. A kinetic model for the internal motions of proteins:> diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.>> Mark Abraham <[EMAIL PROTECTED]>写道：> xi zhao wrote:> > Dear Gromacs users:> > I am a new gromacs user, I want ro calculate r.m.s.i.p> > for exploring similar in motions of two different> > proteins, I need a script or tools to calculate it. I> > need your help!>> I don't know what r.m.s.i.p is. If you want to get help, please define> carefully what you are trying to do - even a link to a journal article> might work. Please read carefully the gromacs manual section that> describes what the utility programs do, in case one of them does it.>> Mark> ___> gmx-users mailing list gmx-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 > 雅虎免费邮箱-3.5G容量，20M附件>>> ___> gmx-users mailing list gmx-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.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Mp3疯狂搜-新歌热歌高速下 ___ 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
回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p
Thank you for your advise!raja <[EMAIL PROTECTED]> 写道： HI Zhao,To compute RMSIP, you have to compute eigenvector using gromacs utilityprogram then from that trajectory you can compute RMSIP using a scriptwhich I got from Tsjerk Wassenaar from this list. You can appraoch him.Regards,B.NatarajOn Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao"<[EMAIL PROTECTED]>said:> Based on the essential dynamics analysis, the similar of the internal> fluctuations in may simulation systems was evaluated by comparing> principal subspace first 10 eigenvectors) of each structural trajectory> by using the root mean square inner product(RMSIP). Amadei, A.,> de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J.> A kinetic model for the internal motions of proteins: diffusion between> multiple harmonic wells. Proteins. 1999. 35, 283-292.> > > Mark Abraham <[EMAIL PROTECTED]>写道： xi zhao wrote:> > Dear Gromacs users:> > I am a new gromacs user, I want ro calculate r.m.s.i.p> > for exploring similar in motions of two different> > proteins, I need a script or tools to calculate it. I> > need your help!> > I don't know what r.m.s.i.p is. If you want to get help, please define> carefully what you are trying to do - even a link to a journal article> might work. Please read carefully the gromacs manual section that> describes what the utility programs do, in case one of them does it.> > Mark> ___> gmx-users mailing list gmx-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> > > > -> 雅虎免费邮箱-3.5G容量，20M附件-- raja[EMAIL PROTECTED]-- http://www.fastmail.fm - I mean, what is it about a decent email service?___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 抢注雅虎免费邮箱-3.5G容量，20M附件！ ___ 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] job opportunity
I am writing to call this community's attention to the job opportunity at http://www.nanoconductor.org/jobs/NCN_at_UIUC_Lead_Scientist.pdf which would involve Gromacs expertise in addition to other software relevant to nanoscience. Thanks for your attention, Eric - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 fax 217-244-2909 ___ 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] velocities
Prasad Gajula wrote: Dear Gromacs Users, I am getting different results for simulations with " gen_vel=yes" and "gen_vel= no". This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200K and last 300K. (with 'gen_vel=no' for all MD) Is it correct? Because I read both 'yes' and 'no' as possibilites in some references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. 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
Re: [gmx-users] Gromacs install question
Qiao Baofu wrote: Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configure 4. make 5 make install The result is that only the following commands are installed in /bin directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, pdb2gmx,protonate,tpbconv, x2top. What wrong with it? who can tell me? Thanks in advance! Probably you didn't do those five steps as described :-) Why is this a problem? Just do it 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
Re: [gmx-users] single point calculation
Reynier Suardiaz del Río wrote: Hi, is my firt question in the list, i have a very simple and posibly a very nonsense question. do i have to use mdrun to performe a single point calculation of a certain conformation? how? is there something to specify in .mdp file? Just do a zero step minimization. Can some body provide me an example of how to use ffscan? with a small molecule if it is possible... Not I. By the way, leaping straight into force field modification before acquiring some experince with gromacs (and/or MD in general) seems to me an excessively masochistic thing to want to do. 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
[gmx-users] Re: The molecule size (jiqing)
Hi:> > > > Two melt models were built for polyethylene (PE) and> > polyvinylmethylether (PVME) melt with PBC condition .> > > > The density of both melt model agree with experimenal value well.But> > when one check the radius of gyration (Rg) of them, both of them were> > too small to accept as follows.> > > > The Rg for PE (C1000) is just 28 angstrom. It means the infinite> > charaterastic ratio (Cinf) for the polymer is just about 2 which is much> > smaller than scatter experimental value about 7.> > > > The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for> > the polymer is just 2.5 which is much smaller than scatter experimental> > value 8-10.> > > > Can these results be accepted?> > > > Is there any fault in force field? gromos96aTwo things,- maybe you need a larger systems- maybe g_gyrate does not take periodicity into account correctly. extract some single molecules and look at them in a viewer, or write your own script to compute Rg.- have you used pbc = full for the simulations? 1.The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. 2. The Rg is anaylzed by my own program, which has been validated. 3.PBC=XYZ > > Usually a garbage result as output means that you had either garbage as> input, or garbage for the algorithm. Find a published article that> describes a similar simulation and adapt their method suitably.> Otherwise describe your method more thoroughly (e.g. how large was the> box, what ensemble did you use, equilibration regime, etc.) and maybe> someone has some judgement they can share with you.> > Mark> > *Hi Mark:*> *Thanks for your advise. Because the PE model is built by one of my > officemate, i did not konw its details.*> ** > *The cell length about my PVME model is 4.5 nm which is big enough for a > PVME chain possesses all trans conformation. The ensemble is NVT with > the control file Pcoupl = no after 10ns NPT simulation to reach the > experimental density. The runtime for NVT is 5ns from which the relax > time for end to end vector is anaylzed. The relax time is about 1ns. So > i think the system has been relaxed enough.*> ** > *Is there any error in my process?*> ** > *Maybe the residue parameter for PVME is also needed for discuss. They are:*> [ VME ] [ atoms ] ; atom type charge cgnr CN Gasteiger CAB CH1 0.142 1 ; CN CAA CH2 0.035 1 ; CN OAD OE -0.352 1 ; CN CAC CH3 0.174 1 ; CN [ bonds ] ; ai aj fu CAA CAB gb_27 CAB OAD gb_53 CAC OAD gb_53 CAB +CAA gb_27 [ angles ] ; ai aj ak fu c0, c1, ... CAA CAB OAD ga_30 CAB OAD CAC ga_10 OAD CAB +CAA ga_30 CAA CAB +CAA ga_15 CAB +CAA +CAB ga_15 [ dihedrals ]; ai aj ak al fu c0, c1, m, ... CAA CAB OAD CAC gd_13 CAA CAB +CAA +CAB gd_34 +CAA CAB OAD CAC gd_13 CAB +CAA +CAB +OAD gd_1 ___ 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: The molecule size (jiqing)
主月 ：） wrote: > Hi: > Two things, > > - maybe you need a larger systems > - maybe g_gyrate does not take periodicity into account correctly. > extract some single molecules and look at them in a viewer, or write > your own script to compute Rg. > - have you used pbc = full for the simulations? > > 1.*The cell length about my PVME model is 4.5 nm which is big enough for > a PVME chain possesses all trans conformation.* Fine, that would be a minimum necessary condition for something that was expected to extend fully. You should actually increase that so that in such a case the opposite ends can't see each other. You need margins at least as large as your largest cut-offs. You can see if this is a potential problem by seeing if any of your monomers do extend in this way. Your experimental system probably had room for about 10^8 such chains end to end, so there is a chance you're comparing apples and oranges here. > *2. The Rg is anaylzed by my own program, which has been validated.* > ** > *3.PBC=XYZ* Has this force field been demonstrated to be effective for this sort of simulation? If not, maybe you've begun to demonstrate that it isn't? 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
[gmx-users] single and double
My system here is an opls-aa protein in a POPE/DMPE membrane with tip4p waters. Prior to adding counterions, grompp yields a net charge of -1.73 and grompp_d yields -2.0. Once I have added counterions, both single and double precision don't give me a warning about a net charge on the system. Either system runs fine for many ns and they don't crash. 1. Is the net charge really as close to 0.0 in the single precision version as it is in the double, or just close enough that there is no warning issued? 2. If single is farther from 0.0, is this a problem? 3. Why does single run faster anyway? I though intel processors treated them the exact same way in terms of the operations that needed to be carried out? Thanks. Chris. ___ 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] periodic boundary condition
Dear David, I tried to use x2top, but it ended up with the following error: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges10: Encad all-atom force field, using full solvent charges 0Looking whether force field file ffG43a1.rtp existsOpening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.rtpGenerating bonds from distances...Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.atpThere are 49 type to mass translationsatom 438---Program x2top, VERSION 3.3Source code file: futil.c, line: 537Fatal error:Library file ffG43a1.n2t not found in current dir nor in default directories.(You can set the directories to search with the GMXLIB path variable)Could you tell me what is wrong? Many thanks!!!CherryDavid van der Spoel <[EMAIL PROTECTED]> wrote: Cherry Y. Yates wrote:> Dear gromacs developers and users,> > I am calculating a nanotube which has periodic boundary condition along > one direction. I wonder how to make an itp file for this system. The > difficulty lies in describing the bond between two end atoms, e.g., two > atoms are bonded in an infinite length system, but are located on the > bottom and top of a unit cell.use x2topand in your mdp file use pbc=full> > Thanks,> > Cherry> > > Get your email and more, right on the new 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-- 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, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.___ 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
