[gmx-users] protein in SDS/water
Dear gmx-users, I would like to setup a simulation of a protein in a mixture SDS/water using GROMACS 3.3.1. I proceeded in this way: - after pdb2gmx, I created with editconf a cubic box of 10 nm per side centered on my protein: editconf -f my_prot.gro -o my_prot_box.gro -bt cubic -box 10 -c - then I used genbox to fill the box with water and to add the desired quantity of SDS (to simulate 3.5 M SDS I added approx. 2000 molecules of SDS to the box). I obtained the coordinates of SDS from a pdb file and then used PRODRG server to create the topology and the coordinate in .gro format. The command was: genbox -cp my_prot_box.gro -cs spc216.gro -ci SDS.gro -nmol 2000 -o my_prot_boxsolv.gro -p my_prot.top The output of this command is a .gro file in which the protein is at the centre of the cubic box, filled with approx. 36000 water molecules and 2000 molecules of SDS. I had a look at it with VMD, and all seems to be OK. The only "strange" thing is that the SDS molecules are not considered as "solvent" molecules. The problem comes when I'm starting to minimize this box. When I use grompp: grompp -f em.mdp -c my_prot_boxsolv.gro -o my_prot_mini.tpr -p my_prot.top the program returns the error: Fatal error: number of coordinates in coordinate file (my_prot_boxsolv.gro, 144801) does not match topology (my_prot.top, 0) I tried to manually edit the .top file by adding the number of SDS molecules under the section [ molecules ], I also added manually "SDS.itp" to the topology file, but all was useless. I don't really know especially why GROMACS claims that the number of coordinates in the topology is 0, since at least the protein is present. What's wrong? I saw many procedures to create mixed solvents for a simulation, but I don't know what is the better one. However, genbox -nmol -ci seems perfect for me and apparently it functions in creating the system. So why the topology file is not updated by genbox? Or in case, could you suggest me a better procedure to add 3.5 M SDS to my protein in water? Thank you and best regards Anna I tried to copy the .top file at the end of the message, but it is too big, so please if you need to see it let me know how to send to you. __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" ___ 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] protein in SDS/water
Anna Marabotti wrote: Dear gmx-users, I would like to setup a simulation of a protein in a mixture SDS/water using GROMACS 3.3.1. I proceeded in this way: - after pdb2gmx, I created with editconf a cubic box of 10 nm per side centered on my protein: editconf -f my_prot.gro -o my_prot_box.gro -bt cubic -box 10 -c - then I used genbox to fill the box with water and to add the desired quantity of SDS (to simulate 3.5 M SDS I added approx. 2000 molecules of SDS to the box). I obtained the coordinates of SDS from a pdb file and then used PRODRG server to create the topology and the coordinate in .gro format. The command was: genbox -cp my_prot_box.gro -cs spc216.gro -ci SDS.gro -nmol 2000 -o my_prot_boxsolv.gro -p my_prot.top The output of this command is a .gro file in which the protein is at the centre of the cubic box, filled with approx. 36000 water molecules and 2000 molecules of SDS. I had a look at it with VMD, and all seems to be OK. The only "strange" thing is that the SDS molecules are not considered as "solvent" molecules. Shrug... that depends on the definition of solvent. The problem comes when I'm starting to minimize this box. When I use grompp: grompp -f em.mdp -c my_prot_boxsolv.gro -o my_prot_mini.tpr -p my_prot.top the program returns the error: Fatal error: number of coordinates in coordinate file (my_prot_boxsolv.gro, 144801) does not match topology (my_prot.top, 0) OK, so probably something is wrong with your [molecules] section. I tried to manually edit the .top file by adding the number of SDS molecules under the section [ molecules ], I also added manually "SDS.itp" to the topology file, but all was useless. I don't really know especially why GROMACS claims that the number of coordinates in the topology is 0, since at least the protein is present. Not if [molecules] is mangled. The order of the directives is quite important. The #include for SDS.itp must come before [molecules] and after the final subsection of any other [molecule] section. See parts of chapter 5 of the manual. Mark What's wrong? I saw many procedures to create mixed solvents for a simulation, but I don't know what is the better one. However, genbox -nmol -ci seems perfect for me and apparently it functions in creating the system. So why the topology file is not updated by genbox? Or in case, could you suggest me a better procedure to add 3.5 M SDS to my protein in water? Thank you and best regards Anna I tried to copy the .top file at the end of the message, but it is too big, so please if you need to see it let me know how to send to you. __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" ___ 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 ___ 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
[gmx-users] Re: -ighn failing with ffamber
Hi Justin, Just to let you know that after reinstalling everything again with Fink it worked fine. I have no idea I hade such a problem. Alan On Mon, Jun 15, 2009 at 23:05, Alan wrote: > Hi Justin, > > Please, confirm this, you mean that this pdb worked for you with '-ignh'? > > Gosh... > > So I may not loosing my mind when I said that it was working before. > > So, I am running: > - Mac Osx 10.5.7 intel. > - Gromacs 4.0.5 (from Fink) with ffamber; > - Compilers from Fink. > > I ran test suite and although I got some fails for complex and > kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite > would fail because oplsaa is working fine here if I do 'pdb2gmx -f > GGG.pdb -ff oplsaa -ignh' > > In any case, many thanks for your attention Justin, > > Alan > > On Mon, Jun 15, 2009 at 20:01, wrote: >> Alan wrote: >>> Thank you Justin, >>> >>> You noticed well that. But this example was built to work without >>> -ignh and to exemplify my problem, because in real case I have this >>> protein and either I can use 'sed' to fix it (mainly H names) I found >>> it annoying sometimes, so why not -ignh? >>> >> >> No idea. I can successfully process your .pdb file with and without -ignh, >> and >> I get the same result (a correct topology) each time. Have you run the test >> suite to validate your installation? Maybe if you post the details of your >> hardware, compilers, OS, etc. someone can spot something that might be >> problematic (i.e., a bug). >> >> -Justin >> >>> Cheers, >>> Alan >>> >>> On Mon, Jun 15, 2009 at 15:51, wrote: >>> Alan wrote: > Hi there, > I am trying to understand why when doing: > > pdb2gmx -f GGG.pdb -ff amber99sb -ignh > > I am getting: > > WARNING: atom H is missing in residue GLY 2 in the pdb file > You might need to add atom H to the hydrogen database of residue > GLY > in the file ff???.hdb (see the manual) > I don't know why this is failing, but from the looks of your .pdb file, you have all the atoms you need, properly named and everything. Why do you need -ignh? -Justin > --- > Program pdb2gmx, VERSION 4.0.5 > Source code file: pdb2top.c, line: 704 > Fatal error: > There were 1 missing atoms in molecule Protein_G, if you want to use > this incomplete topology anyhow, use the option -missing > --- > > in /sw/share/gromacs/top/ffamber99sb.hdb I have: > > GLY 2 > 1 1 H N -C CA > 2 6 HA CA N C > > And I see nothing wrong with that. > > in /sw/share/gromacs/top/ffamber99sb.rtp: > > [ GLY ] > [ atoms ] > N amber99_34 -0.41570 1 > H amber99_17 0.27190 2 > CA amber99_11 -0.02520 3 > HA1 amber99_19 0.06980 4 > HA2 amber99_19 0.06980 5 > C amber99_2 0.59730 6 > O amber99_41 -0.56790 7 > > Which is pretty OK too. > > Besides, I don't get any error for NGLY or CGLY. Only "atom H is > missing in residue GLY 2". If I mess with ffamber99sb.hdb for GLY I > got others messages stating the other missing atoms. > OPLS, which is very similar, works fine. > > The pdb is as simple as this: > ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 > ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 > ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 > ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 > ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 > ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 > ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 > ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 > ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 > ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 > ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 > ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 > ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 > ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 > ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 > ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 > ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 > ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 > ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 > ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 > ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 > ATOM 22 C CGLYG 3 67.808 -1.80
Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
hi Justin,
I tried the NVT once with certain changes in the parameter file. Now its
finished the 10 ps. But I have used the charge as the same from the
antechamber program. Do you think the result will be reliable? Please check
the mdp file attached for NVT.
The .mdp file seems reasonable. QM charges are not necessarily the end result
in Gromos parameterization. In fact, such calculations are often unnecessary.
In my experience, assigning charges based on functional groups already present
in the force field is often a reasonable starting point. But in any case, you
must always verify your results and, in the end, follow the same
parameterization scheme as the original force field (which, in the case of the
Gromos force fields, does not include QM charge calculations).
-Justin
Thnaks for your help Aswathy Dept. Biotechnology Ext. 3108
- Original Message - From: "Justin A. Lemkul" To:
"Gromacs Users' List" Sent: Tuesday, June 16, 2009
5:29:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re:
[gmx-users] problem in ngmx
Ms. Aswathy S wrote:
My point was I have set the NVT equilibration as 10 ps. But it run only 5.4
ps. when I checked the temperature It was also stabilized at 5.4 ps. That
is why I went ahead with NPT.Can we consider OK, if the equilibration stops
before the time we set??
Absolutely not. If any MD process stops before it is supposed to, that means
it crashed.
I am following some literatures, from that i thought first I should
equlibrate the water then give restraint to water and equilibrate the
protein further. thats why I did in that way???I will check that once
again.
Not necessary. In all the recent literature I have seen, position restraints
are placed on the protein, while the solvent is free to move. After some
time, all restraints are removed and production MD is conducted.
In any case, your problem occurs before you get to this stage. Your NVT is
failing; you need to figure out why.
-Justin
Dept. Biotechnology Ext. 3108
- Original Message - From: "Justin A. Lemkul" To:
"Gromacs Users' List" Sent: Tuesday, June 16, 2009
5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re:
[gmx-users] problem in ngmx
Ms. Aswathy S wrote:
sorry..forgot to attach the file...
After my NVT I have checked the PE of the system..It was stabilised..So I
thought everything was fine till NVT. How can i check whetehr its a
problem with NVT?Is that the box type could be the resaon?
Convergence of PE is a good indicator that energy minimization is complete.
The purpose of NVT is to stabilize the temperature of the system. My main
problem with what you said before was that you did 10 ps of NVT in 2600
steps. This seems wrong, given the fractional nature of the time step
required to do such a procedure. Use gmxcheck on the .trr or .edr file to
see how many frames it finds; verify that you have a complete trajectory.
Also, in the .mdp file you attached, you are applying position restraints
to the water in your system. If you are not also restraining the protein,
it is probably colliding with the water, causing the explosion you are
seeing. Why are you restraining water during NPT equilibration, or during
MD for that matter?
-Justin
Dept. Biotechnology Ext. 3108
- Original Message - From: "Justin A. Lemkul"
To: "Discussion list for GROMACS users" Sent:
Tuesday, June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi Subject: Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
Hi,
In my NPT step I think there is some poblem. i am getting the follo:
error. I have used box as cubic I s that could be the problem
Please see the md,..mop file
You haven't posted the .mdp file. In any case, see my previous message.
I think something went wrong during NVT. Here, the messages indicate
that your box is exploding. See, for example:
http://oldwiki.gromacs.org/index.php/blowing_up
-Justin
Please try to hepl me.. Box[2]={ nan, nan, nan}
Can not fix pbc. Warning: Only triclinic boxes with the first vector
parallel to the x-axis and the second vector in the xy-plane are
supported. Box (3x3): Box[0]={ nan, nan,
nan} Box[ 1]={ nan, nan, nan} Box[2]={
nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the
first vector parallel to the x-axis and the second vector in the
xy-plane are supported. Box (3x3): Box[0]={ nan,
nan, nan} Box[1]={ nan, nan, nan} Box[
2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic
boxes with the first vector parallel to the x-axis and the second
vector in the xy-plane are supported. Box (3x3): Box[0]={
nan, nan, nan} Box[1]={ nan, nan,
nan} Box[2]={ nan, nan, nan} Can not fix pbc. Warning: Only
triclinic boxes with the first vector paral
[gmx-users] programmes to have in double precision besides mdrun_d
Hi there, I usually create only mdrun_d (double precision), although I am not a hard user, however, doing some usage lately, I caught asking me if 'grompp' should be double too, and then what else. So, is there any reason for others programme to go double besides mdrun? If so, which programmes one would suggest, why? Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< ___ 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] programmes to have in double precision besides mdrun_d
Alan wrote: Hi there, I usually create only mdrun_d (double precision), although I am not a hard user, however, doing some usage lately, I caught asking me if 'grompp' should be double too, and then what else. So, is there any reason for others programme to go double besides mdrun? If so, which programmes one would suggest, why? I would think everything would have to be in double precision - grompp to generate the proper input; editconf, genbox, etc. to write the correct precision; all of the analysis tools to read the double-precision files produced by mdrun_d...but I've never had much experience with double precision, so I can't be 100% on that. -Justin Many thanks in advance. Alan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] PBC
Remember that for PBC=xyz, the neighbor search is faster, so I suggest using PBC with a very large box. --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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] programmes to have in double precision besides mdrun_d
Hi, Nothing needs to be double precision. Why do you want mdrun in double precision? The only common reason for this is normal mode analysis, in which case you need all the tools involved in double precision. For normal MD simulation there is nearly never a need for double precision. Actually mdrun is the only program where performance really matters, so compiling all other programs in double precision is a not an issue. All Gromacs programs independently of the compilation can read both single and double precision files. Berk > Date: Wed, 17 Jun 2009 07:04:44 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] programmes to have in double precision besides > mdrun_d > > > > Alan wrote: > > Hi there, > > > > I usually create only mdrun_d (double precision), although I am not a > > hard user, however, doing some usage lately, I caught asking me if > > 'grompp' should be double too, and then what else. > > > > So, is there any reason for others programme to go double besides > > mdrun? If so, which programmes one would suggest, why? > > > > I would think everything would have to be in double precision - grompp to > generate the proper input; editconf, genbox, etc. to write the correct > precision; all of the analysis tools to read the double-precision files > produced > by mdrun_d...but I've never had much experience with double precision, so I > can't be 100% on that. > > -Justin > > > Many thanks in advance. > > > > Alan > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ 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] Electrostatic forces
Hi, I think there is still a general issue with optimizing the PME settings (or settings for any electrostatics method) for MD simulations. The question is what exactly one should optimize. If you do a single point calculation, you might only want to minimize the force error. But for MD you might also want good energy conservation. Optimizing the RMS force is certainly not the best choice, since that would lead to a large ewald_rtol, which gives small errors before the cut-off and on most of the long-range part, but large errors just beyond the cut-off. This will lead to bad energy conservation. Even an absolute force error will probably lead to a too large ewald_rtol. Berk _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ 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] Electrostatic forces
Hello Mark, the point why I ask all this questions is that my final goal is to enhance the SPME algorithm in Gromacs. As it is well know, that SPME is not momentum conserving in case the forces are derived with analytical differentiation, that means the reciprocal forces stem from the derivative of the reciprocal sum after performing the FFTs in reciprocal space and back again. This just requires 2FFTs per step. In contrast the ik differentiation allows to obtain forces that conserve the momentum. However in this case 4FFT are required: 1 into reciprocal space and 3 back to gather every component of the force. We have tested this two implementations of the SPME and realized that under the condition of a certain accuracy, the analytical differentiation is not always the cheaper one as expected due to the less number of FFTs. Sometimes the higher number of FFTs is balanced out by the smaller interpolation order or reciprocal space cut-off required to reach the accuracy the same accuracy as in case of analytical differentiation. It is also sad, that the PPPM algorithm is not working correctly, because this would be the "best" way of calculation electrostatic forces. The authors showed that the Green Function that is determined by the interpolation scheme and used for their derivation of the PPPM is mathematically the optimal one. So I also would like to correct the implementation of the PPPM algorithm to provide a correct implementation of the virial calculation. And by the way, the error of the RMSF depens on the charge density, beta, interpolation order and cutoffs in real and reciprocal space. This means as soon as you have the optimal set for a given charge density. So you can apply this parameters to all systems with the same charge density independent of its actual size and charge distribution, only the charge density has to match. Flo * Mark Abraham [2009-06-17 16:11:14 +1000]: Florian Dommert wrote: * Mark Abraham [2009-06-17 15:31:43 +1000]: Florian Dommert wrote: * Mark Abraham [2009-06-17 14:14:22 +1000]: Florian Dommert wrote: However I am very confident and in case of success, that there will be soon an error estimate for the Ewald Sum available, which will be the first step to the an implementation a tuning routine for the SPME paramters to achieve optimal balance between performance and accuracy ;) I've already implemented a version of mdrun that actually computes the RMS error in the force components under PME, and am planning to release it soon. That is very nice to hear, how do you compute the error ? By comparing to an Ewald Sum ? Holding beta fixed, I compare force components with those from a converged real-space summation and high Fourier grid density & interpolation order. So you have to perform a very costly simulation for every system, when you gather the reference force ? Actually, both the reference force run and the parameter scan runs are invocations of "mdrun -rerun". I haven't notice the former to be very costly, but there's a trade-off involved. To converge the components to machine precision might indeed be very costly, but one doesn't need to go to that extreme to estimate that the average RMS force error over the test trajectory is 1e-4 (or whatever). And which beta do you choose, because if you take the right choice you can decrease the computational cost extremely. Yep. Having chosen a desired accuracy, you have to scan beta (with ewald_rtol and rcoulomb) and then scan the grid densities to find point(s) with acceptable accuracy and minimal cost. This is not such an extreme problem once you have some guidance from previous optimizations. So theoretically at first you have to find the right beta by sampling through the corresponding parameter space with a fixed Interpolation order and grid size. In the optimal range a change of beta within 0.1 will yield a difference in the error of about 10-1 this trend continues around +/- 0.5 of the optimal value for beta. OK, I'll have to take your word for that, since I haven't looked at the maths in that detail. It's certainly well-known (e.g. original PME papers) that a correct choice of parameters can swing orders of magnitude of computational cost for given accuracy, or vice-versa. Mark ___ 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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: ht
Re: [gmx-users] problem in ngmx
On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: > > The .mdp file seems reasonable. QM charges are not necessarily the end > result in Gromos parameterization. In fact, such calculations are often > unnecessary. In my experience, assigning charges based on functional groups > already present in the force field is often a reasonable starting point. > But in any case, you must always verify your results and, in the end, > follow the same parameterization scheme as the original force field (which, > in the case of the Gromos force fields, does not include QM charge > calculations). I've run hundreds of QM charge calculations. in many cases, they are remarkably similar to the gromos charges... cheers, marc ___ 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
[gmx-users] regarding genhydro.c/pdb2gmx algorithm
Dear users I am trying to know how gromcas is adding hydrogens so fastly and for it I have downloaded the source code also, but not getting any thing. Can any one please brief me so that I can initiate by myself. Thanx in advance with regards PRASUN (ASHOKA) ___ 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] regarding genhydro.c/pdb2gmx algorithm
prasun kumar wrote: Dear users I am trying to know how gromcas is adding hydrogens so fastly and for it I have downloaded the source code also, but not getting any thing. Can any one please brief me so that I can initiate by myself. The algorithms are described in the manual. Mark ___ 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] problem in ngmx
Marc F. Lensink wrote: On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: The .mdp file seems reasonable. QM charges are not necessarily the end result in Gromos parameterization. In fact, such calculations are often unnecessary. In my experience, assigning charges based on functional groups already present in the force field is often a reasonable starting point. But in any case, you must always verify your results and, in the end, follow the same parameterization scheme as the original force field (which, in the case of the Gromos force fields, does not include QM charge calculations). I've run hundreds of QM charge calculations. in many cases, they are remarkably similar to the gromos charges... Agreed. The point I was trying to make (perhaps poorly) was that simply running a QM charge calculation and calling it done is not the right track. I got the impression from the original post that charges were assigned and a simulation conducted without any validation of those parameters. -Justin cheers, marc ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
[gmx-users] Re: protein in SDS/water
Dear Mark, thank you very much for suggestions. I'm pasting here an "extract" of the .top file I used during the grompp process (the complete one is too big to be sent to the mailing list, as I told yesterday - the dots indicate that I delete the information here, but they are present in the original file). As you can see, I added manually the #include for SDS.itp before [ molecules ] and "SDS" under [ moleculetype ] and [ molecules ] section. Maybe I made a trivial error, but I can't find it. All lines under [ atoms], [bonds], [pairs], [angles] and [dihedral] sections refer only to the protein. Moreover, it is quite strange to me that when I'm doing genbox, the top file is not updated automatically. I copied the SDS.itp file from PRODRG in the directory ../gromacs/share/top containing all others .itp files, but it seems that the program does not find information for SDS to include automatically in the .top file Many thanks for help Kind regards Anna Here the my_prot.top file (extract): ; ; File 'my_prot.top' was generated ; By user: anna (62867) ; On host: bioserv1.isa.cnr.it ; At date: Tue Jun 16 16:15:08 2009 ; ; This is your topology file ; "The World is a Friendly Place" (Magnapop) ; ; Include forcefield parameters #include "ffG43a1.itp" [ moleculetype ] ; Namenrexcl Protein 3 SDS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 3 H 1SER H2 1 0.248 1.008 ; qtot 0.625 . . 2280 C229GLU C980 0.27 12.011 ; qtot -6.73 2281 OM229GLU O1980 -0.63515.9994 ; qtot -7.365 2282 OM229GLU O2980 -0.63515.9994 ; qtot -8 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_2 1 5 2gb_20 ... ... 2275 2276 2gb_26 2276 2277 2gb_26 2277 2278 2gb_5 2277 2279 2gb_5 2280 2281 2gb_5 2280 2282 2gb_5 [ pairs ] ; aiaj functc0c1c2c3 1 7 1 110 1 111 1 ... ... 2273 2275 1 2273 2280 1 2274 2277 1 2275 2278 1 2275 2279 1 2275 2281 1 2275 2282 1 2276 2280 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 2ga_9 2 1 4 2ga_9 2 1 5 2ga_10 3 1 4 2ga_9 3 1 5 2ga_10 . . 2275 2276 2277 2ga_14 2276 2277 2278 2ga_21 2276 2277 2279 2ga_21 2278 2277 2279 2ga_37 2274 2280 2281 2ga_21 2274 2280 2282 2ga_21 2281 2280 2282 2ga_37 [ dihedrals ] ; aiajakal functc0c1c2 c3c4 c5 2 1 5 9 1gd_14 1 5 6 7 1gd_17 1 5 911 1gd_20 5 6 7 8 1gd_12 5 91113 1gd_4 .. .. 2270 2272 2274 2280 1gd_19 2272 2274 2275 2276 1gd_17 2272 2274 2280 2282 1gd_20 2274 2275 2276 2277 1gd_17 2275 2276 2277 2279 1gd_20 [ dihedrals ] ; aiajakal functc0c1c2 c3 5 1 9 6 2gi_2 9 51110 2gi_1 11 91312 2gi_1 14131615 2gi_1 16141817 2gi_1 18162019 2gi_2 20182221 2gi_1 .. .. 2260 2256 2258 2261 2gi_1 2262 2249 2264 2263 2gi_1 2264 2262 2266 2265 2gi_1 2266 2264 2270 2267 2gi_2 2270 2266 2272 2271 2gi_1 2272 2270 2274 2273 2gi_1 2274 2272 2280 2275 2gi_2 2276 2279 2278 2277 2gi_1 2280 2274 2282 2281 2gi_1 ; Include Positi
Re: [gmx-users] Re: protein in SDS/water
Anna Marabotti wrote: Dear Mark, thank you very much for suggestions. I'm pasting here an "extract" of the .top file I used during the grompp process (the complete one is too big to be sent to the mailing list, as I told yesterday - the dots indicate that I delete the information here, but they are present in the original file). As you can see, I added manually the #include for SDS.itp before [ molecules ] and "SDS" under [ moleculetype ] and [ molecules ] section. Maybe I made a trivial error, but I can't find it. All lines under [ atoms], [bonds], [pairs], [angles] and [dihedral] sections refer only to the protein. Moreover, it is quite strange to me that when I'm doing genbox, the top file is not updated automatically. I copied the SDS.itp file from PRODRG in the directory ../gromacs/share/top containing all others .itp files, but it seems that the program does not find information for SDS to include automatically in the .top file Many thanks for help Kind regards Anna Here the my_prot.top file (extract): ; ; File 'my_prot.top' was generated ; By user: anna (62867) ; On host: bioserv1.isa.cnr.it ; At date: Tue Jun 16 16:15:08 2009 ; ; This is your topology file ; "The World is a Friendly Place" (Magnapop) ; ; Include forcefield parameters #include "ffG43a1.itp" [ moleculetype ] ; Namenrexcl Protein 3 SDS 3 Here's your problem. You've defined two molecule types in one moleculetype directive. Look in SDS.itp - you'll likely find the moleculetype is defined there as well. -Justin [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 3 H 1SER H2 1 0.248 1.008 ; qtot 0.625 . . 2280 C229GLU C980 0.27 12.011 ; qtot -6.73 2281 OM229GLU O1980 -0.63515.9994 ; qtot -7.365 2282 OM229GLU O2980 -0.63515.9994 ; qtot -8 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_2 1 5 2gb_20 ... ... 2275 2276 2gb_26 2276 2277 2gb_26 2277 2278 2gb_5 2277 2279 2gb_5 2280 2281 2gb_5 2280 2282 2gb_5 [ pairs ] ; aiaj functc0c1c2c3 1 7 1 110 1 111 1 ... ... 2273 2275 1 2273 2280 1 2274 2277 1 2275 2278 1 2275 2279 1 2275 2281 1 2275 2282 1 2276 2280 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 2ga_9 2 1 4 2ga_9 2 1 5 2ga_10 3 1 4 2ga_9 3 1 5 2ga_10 . . 2275 2276 2277 2ga_14 2276 2277 2278 2ga_21 2276 2277 2279 2ga_21 2278 2277 2279 2ga_37 2274 2280 2281 2ga_21 2274 2280 2282 2ga_21 2281 2280 2282 2ga_37 [ dihedrals ] ; aiajakal functc0c1c2 c3c4 c5 2 1 5 9 1gd_14 1 5 6 7 1gd_17 1 5 911 1gd_20 5 6 7 8 1gd_12 5 91113 1gd_4 .. .. 2270 2272 2274 2280 1gd_19 2272 2274 2275 2276 1gd_17 2272 2274 2280 2282 1gd_20 2274 2275 2276 2277 1gd_17 2275 2276 2277 2279 1gd_20 [ dihedrals ] ; aiajakal functc0c1c2 c3 5 1 9 6 2gi_2 9 51110 2gi_1 11 91312 2gi_1 14131615 2gi_1 16141817 2gi_1 18162019 2gi_2 20182221 2gi_1 .. .. 2260 2256 2258 2261 2gi_1 2262 2249 2264 2263 2gi_1 2264 2262 2266 2265 2gi_1 2266 2264 2270 2267 2g
RE: [gmx-users] programmes to have in double precision besides mdrun_d
On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote: > Hi, > > Nothing needs to be double precision. > > Why do you want mdrun in double precision? > The only common reason for this is normal mode analysis, > in which case you need all the tools involved in double precision. > For normal MD simulation there is nearly never a need for > double precision. If you want to run accurate NVE simulations, double precision is important. If you use thermostats, then there is no need for double precision. Also, I have found that double precision can be nice for energy minimization since it can handle more pathological cases than single precision. Still, usually it doesn't matter much whether the starting point was prepared in single or double precision. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ 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] programmes to have in double precision besides mdrun_d
Jussi Lehtola skrev: On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote: Hi, Nothing needs to be double precision. Why do you want mdrun in double precision? The only common reason for this is normal mode analysis, in which case you need all the tools involved in double precision. For normal MD simulation there is nearly never a need for double precision. If you want to run accurate NVE simulations, double precision is important. If you use thermostats, then there is no need for double precision. I can testify to that. Without double precision I've had problems with drifting total energy when doing non-periodic NVE. /Erik Also, I have found that double precision can be nice for energy minimization since it can handle more pathological cases than single precision. Still, usually it doesn't matter much whether the starting point was prepared in single or double precision. -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, 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://xray.bmc.uu.se/molbiophys ___ 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: protein in SDS/water
Anna Marabotti wrote: Dear Mark, thank you very much for suggestions. I'm pasting here an "extract" of the .top file I used during the grompp process (the complete one is too big to be sent to the mailing list, as I told yesterday - the dots indicate that I delete the information here, but they are present in the original file). As you can see, I added manually the #include for SDS.itp before [ molecules ] and "SDS" under [ moleculetype ] and [ molecules ] section. Maybe I made a trivial error, but I can't find it. All lines under [ atoms], [bonds], [pairs], [angles] and [dihedral] sections refer only to the protein. Moreover, it is quite strange to me that when I'm doing genbox, the top file is not updated automatically. I copied the SDS.itp file from PRODRG in the directory ../gromacs/share/top containing all others .itp files, but it seems that the program does not find information for SDS to include automatically in the .top file Many thanks for help Kind regards Anna Here the my_prot.top file (extract): ; ; File 'my_prot.top' was generated ; By user: anna (62867) ; On host: bioserv1.isa.cnr.it ; At date: Tue Jun 16 16:15:08 2009 ; ; This is your topology file ; "The World is a Friendly Place" (Magnapop) ; ; Include forcefield parameters #include "ffG43a1.itp" [ moleculetype ] ; Namenrexcl Protein 3 SDS 3 This is wrong. [moleculetype] declares the existence of a new type of molecule, whose name follows. A subsequent [moleculetype] ends the previous molecule type and starts a new one. Thus only one type of molecule can be described in a [moleculetype] section. (My previous post erroneously referred to [molecule] sections, sorry!) The entries in [molecules] at the end refer to the names given in [moleculetype] sections. Mark [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 3 H 1SER H2 1 0.248 1.008 ; qtot 0.625 . . 2280 C229GLU C980 0.27 12.011 ; qtot -6.73 2281 OM229GLU O1980 -0.63515.9994 ; qtot -7.365 2282 OM229GLU O2980 -0.63515.9994 ; qtot -8 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_2 1 5 2gb_20 ... ... 2275 2276 2gb_26 2276 2277 2gb_26 2277 2278 2gb_5 2277 2279 2gb_5 2280 2281 2gb_5 2280 2282 2gb_5 [ pairs ] ; aiaj functc0c1c2c3 1 7 1 110 1 111 1 ... ... 2273 2275 1 2273 2280 1 2274 2277 1 2275 2278 1 2275 2279 1 2275 2281 1 2275 2282 1 2276 2280 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 2ga_9 2 1 4 2ga_9 2 1 5 2ga_10 3 1 4 2ga_9 3 1 5 2ga_10 . . 2275 2276 2277 2ga_14 2276 2277 2278 2ga_21 2276 2277 2279 2ga_21 2278 2277 2279 2ga_37 2274 2280 2281 2ga_21 2274 2280 2282 2ga_21 2281 2280 2282 2ga_37 [ dihedrals ] ; aiajakal functc0c1c2 c3c4 c5 2 1 5 9 1gd_14 1 5 6 7 1gd_17 1 5 911 1gd_20 5 6 7 8 1gd_12 5 91113 1gd_4 .. .. 2270 2272 2274 2280 1gd_19 2272 2274 2275 2276 1gd_17 2272 2274 2280 2282 1gd_20 2274 2275 2276 2277 1gd_17 2275 2276 2277 2279 1gd_20 [ dihedrals ] ; aiajakal functc0c1c2 c3 5 1 9 6 2gi_2 9 51110 2gi_1 11 91312 2gi_1 14131615 2gi_1 16141817 2gi_1 18162019 2gi_2 2018222
Re: [gmx-users] Electrostatic forces
* Berk Hess [2009-06-17 13:54:07 +0200]: Hi, I think there is still a general issue with optimizing the PME settings (or settings for any electrostatics method) for MD simulations. The question is what exactly one should optimize. If you do a single point calculation, you might only want to minimize the force error. But for MD you might also want good energy conservation. Optimizing the RMS force is certainly not the best choice, since that would lead to a large ewald_rtol, which gives small errors before the cut-off and on most of the long-range part, but large errors just beyond the cut-off. This will lead to bad energy conservation. Even an absolute force error will probably lead to a too large ewald_rtol. Hi, increasing interpolation order and grid size, the optimal beta grows and therefore ewald_rtol decreases. So increasing accuracy corresponds to a descreasing rtol and finally optimized energy conservation. But there arise other problems like a strongly differing charge density in a simulation, that affects the error in the forces considerably. Flo Berk _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx ___ 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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! pgpdGCq0Gy3O9.pgp Description: PGP signature ___ 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] problem in ngmx
Ok. You meant I have to cross check these parameters before getting in to simulation.I will do that Thank you very much for your replies. Dept. Biotechnology Ext. 3108 - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, June 17, 2009 6:35:01 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx Marc F. Lensink wrote: > On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote: >> The .mdp file seems reasonable. QM charges are not necessarily the end >> result in Gromos parameterization. In fact, such calculations are often >> unnecessary. In my experience, assigning charges based on functional groups >> already present in the force field is often a reasonable starting point. >> But in any case, you must always verify your results and, in the end, >> follow the same parameterization scheme as the original force field (which, >> in the case of the Gromos force fields, does not include QM charge >> calculations). > > I've run hundreds of QM charge calculations. in many cases, they are > remarkably similar to the gromos charges... > Agreed. The point I was trying to make (perhaps poorly) was that simply running a QM charge calculation and calling it done is not the right track. I got the impression from the original post that charges were assigned and a simulation conducted without any validation of those parameters. -Justin > cheers, > marc > ___ > 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 > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 ___ 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
[gmx-users] Re: protein in SDS/water
Hi, i think another problem lies here: ; Include water topology > #include "spc.itp" > . > > ; Include generic topology for ions > #include "ions.itp" > > ; Include topology for SDS > #include "SDS.itp" > > [ system ] > ; Name > Protein in water with SDS > > [ molecules ] > ; Compound#mols > Protein 1 > SDS2000 > SOL 36173 You have defined your Protein, then the water, then ions and then SDS. But in [ molecules ] you have the order Protein - SDS - water; but these two orders must be the same. -> Delete the line, which Justin suggested und put the *#include "SDS.itp"* before the *#include "spc.itp"*, then i think all must be fine. Thomas > > > -- > > Message: 5 > Date: Wed, 17 Jun 2009 09:11:29 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: protein in SDS/water > To: Discussion list for GROMACS users > Message-ID: <4a38eb81.6000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Anna Marabotti wrote: >> Dear Mark, >> thank you very much for suggestions. I'm pasting here an "extract" of the >> .top file I used during the grompp >> process (the complete one is too big to be sent to the mailing list, as I >> told yesterday - the dots indicate >> that I delete the information here, but they are present in the original >> file). As you can see, I added >> manually the #include for SDS.itp before [ molecules ] and "SDS" under [ >> moleculetype ] and [ molecules ] >> section. Maybe I made a trivial error, but I can't find it. All lines under >> [ atoms], [bonds], [pairs], >> [angles] and [dihedral] sections refer only to the protein. >> Moreover, it is quite strange to me that when I'm doing genbox, the top file >> is not updated automatically. I >> copied the SDS.itp file from PRODRG in the directory ../gromacs/share/top >> containing all others .itp files, >> but it seems that the program does not find information for SDS to include >> automatically in the .top file >> >> Many thanks for help >> Kind regards >> Anna >> >> Here the my_prot.top file (extract): >> >> ; >> ; File 'my_prot.top' was generated >> ; By user: anna (62867) >> ; On host: bioserv1.isa.cnr.it >> ; At date: Tue Jun 16 16:15:08 2009 >> ; >> ; This is your topology file >> ; "The World is a Friendly Place" (Magnapop) >> ; >> ; Include forcefield parameters >> #include "ffG43a1.itp" >> >> [ moleculetype ] >> ; Namenrexcl >> Protein 3 >> SDS 3 >> > > Here's your problem. You've defined two molecule types in one moleculetype > directive. Look in SDS.itp - you'll likely find the moleculetype is defined > there as well. > > -Justin > >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass typeB >> chargeB massB >> 1 NL 1SER N 1 0.12914.0067 ; qtot >> 0.129 >> 2 H 1SER H1 1 0.248 1.008 ; qtot >> 0.377 >> 3 H 1SER H2 1 0.248 1.008 ; qtot >> 0.625 >> >> . >> >> . >> 2280 C229GLU C980 0.27 12.011 ; qtot >> -6.73 >> 2281 OM229GLU O1980 -0.63515.9994 ; qtot >> -7.365 >> 2282 OM229GLU O2980 -0.63515.9994 ; qtot >> -8 >> >> [ bonds ] >> ; aiaj functc0c1c2c3 >> 1 2 2gb_2 >> 1 3 2gb_2 >> 1 4 2gb_2 >> 1 5 2gb_20 >> ... >> ... >> 2275 2276 2gb_26 >> 2276 2277 2gb_26 >> 2277 2278 2gb_5 >> 2277 2279 2gb_5 >> 2280 2281 2gb_5 >> 2280 2282 2gb_5 >> >> [ pairs ] >> ; aiaj functc0c1c2c3 >> 1 7 1 >> 110 1 >> 111 1 >> ... >> ... >> 2273 2275 1 >> 2273 2280 1 >> 2274 2277 1 >> 2275 2278 1 >> 2275 2279 1 >> 2275 2281 1 >> 2275 2282 1 >> 2276 2280 1 >> >> [ angles ] >> ; aiajak functc0c1c2 >> c3 >> 2 1 3 2ga_9 >> 2 1 4 2ga_9 >> 2 1 5 2ga_10 >> 3 1 4 2ga_9 >> 3 1 5 2ga_10 >> . >> . >> 2275 2276 2277 2ga_14 >> 2276 2277 2278 2ga_21 >> 2276 2277 2279 2ga_21 >> 2278
Re: [gmx-users] Re: protein in SDS/water
Thomas Schlesier wrote: Hi, i think another problem lies here: ; Include water topology #include "spc.itp" . ; Include generic topology for ions #include "ions.itp" ; Include topology for SDS #include "SDS.itp" [ system ] ; Name Protein in water with SDS [ molecules ] ; Compound#mols Protein 1 SDS2000 SOL 36173 You have defined your Protein, then the water, then ions and then SDS. But in [ molecules ] you have the order Protein - SDS - water; but these two orders must be the same. -> Delete the line, which Justin suggested und put the *#include "SDS.itp"* before the *#include "spc.itp"*, then i think all must be fine. I used to think this was true, too. But it was pointed out to me that the order of the #includes does not matter, only the order in which the species appear in the [ molecules ] section. -Justin Thomas -- Message: 5 Date: Wed, 17 Jun 2009 09:11:29 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Re: protein in SDS/water To: Discussion list for GROMACS users Message-ID: <4a38eb81.6000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear Mark, thank you very much for suggestions. I'm pasting here an "extract" of the .top file I used during the grompp process (the complete one is too big to be sent to the mailing list, as I told yesterday - the dots indicate that I delete the information here, but they are present in the original file). As you can see, I added manually the #include for SDS.itp before [ molecules ] and "SDS" under [ moleculetype ] and [ molecules ] section. Maybe I made a trivial error, but I can't find it. All lines under [ atoms], [bonds], [pairs], [angles] and [dihedral] sections refer only to the protein. Moreover, it is quite strange to me that when I'm doing genbox, the top file is not updated automatically. I copied the SDS.itp file from PRODRG in the directory ../gromacs/share/top containing all others .itp files, but it seems that the program does not find information for SDS to include automatically in the .top file Many thanks for help Kind regards Anna Here the my_prot.top file (extract): ; ; File 'my_prot.top' was generated ; By user: anna (62867) ; On host: bioserv1.isa.cnr.it ; At date: Tue Jun 16 16:15:08 2009 ; ; This is your topology file ; "The World is a Friendly Place" (Magnapop) ; ; Include forcefield parameters #include "ffG43a1.itp" [ moleculetype ] ; Namenrexcl Protein 3 SDS 3 Here's your problem. You've defined two molecule types in one moleculetype directive. Look in SDS.itp - you'll likely find the moleculetype is defined there as well. -Justin [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 3 H 1SER H2 1 0.248 1.008 ; qtot 0.625 . . 2280 C229GLU C980 0.27 12.011 ; qtot -6.73 2281 OM229GLU O1980 -0.63515.9994 ; qtot -7.365 2282 OM229GLU O2980 -0.63515.9994 ; qtot -8 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_2 1 5 2gb_20 ... ... 2275 2276 2gb_26 2276 2277 2gb_26 2277 2278 2gb_5 2277 2279 2gb_5 2280 2281 2gb_5 2280 2282 2gb_5 [ pairs ] ; aiaj functc0c1c2c3 1 7 1 110 1 111 1 ... ... 2273 2275 1 2273 2280 1 2274 2277 1 2275 2278 1 2275 2279 1 2275 2281 1 2275 2282 1 2276 2280 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 2ga_9 2 1 4 2ga_9 2 1 5 2ga_10 3 1 4 2ga_9 3 1 5 2ga_10 . . 2275 2276 2277 2ga_14 2276 2277 2278 2ga_21 2276 2277 2279 2ga_21 2278 2277 2279 2ga_37 2274 2280 2281 2ga_21 2274 2280 2282 2ga_21 2281 2280 2282 2ga_37 [ dihedrals ] ; aiaj
RE: [gmx-users] programmes to have in double precision besides mdrun_d
> Date: Wed, 17 Jun 2009 15:17:53 +0200 > From: er...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] programmes to have in double precision besides > mdrun_d > > Jussi Lehtola skrev: > > On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote: > > > >> Hi, > >> > >> Nothing needs to be double precision. > >> > >> Why do you want mdrun in double precision? > >> The only common reason for this is normal mode analysis, > >> in which case you need all the tools involved in double precision. > >> For normal MD simulation there is nearly never a need for > >> double precision. > >> > > > > If you want to run accurate NVE simulations, double precision is > > important. If you use thermostats, then there is no need for double > > precision. > > > > > I can testify to that. Without double precision I've had problems with > drifting total energy when doing non-periodic NVE. > Indeed, this is correct. But I guess this falls into the category nearly never. On the other hand, there are so many Gromacs users nowadays, there nearly never is nearly never zero users. > /Erik > > Also, I have found that double precision can be nice for energy > > minimization since it can handle more pathological cases than single > > precision. Still, usually it doesn't matter much whether the starting > > point was prepared in single or double precision. > > That's true. It would be nice if we could make the single precision code handle such cases better (force capping?). Berk _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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
[gmx-users] covalent bond lookup table
Dear Gromacs users, I need to produce a list of the covalent bonds of my protein structure in the format: Atom1 Atom2 binding energy 12 50 kcal/mol 13 150 kcal/mol ... The binding energy is not the potential calculated by gromacs' force field but the diatomic binding energies available in the literature I actually already have a list of the covalent bonds like this Atom1 Atom2 12 13 ... and a table with the binding energies of each bond type like this bond type binding energy C-C 150 kcal/mol C=C 200 kcal/mol C-H 100 kcal/mol but, in order to create such file, I'd need to build a script that scans my pdb looking for the atom types and working out whether in between there's a single or double bond according to the aminoacid's chemical formula. Thus, I was wondering if Gromacs can perform any operation to make my work less painful. Is there a command or an option able to output a similar file? It would be already of great help to have a simple lookup table like this Atom1 Atom2 single-or-double-bond? 12single 13double ... I took a quick look to the files ffoplsaa.* but I couldn't quite find what I was looking for. Maybe the field "name" of the *.itp file could be useful. Can you think of an easy solution? Thanks, Stefano ___ 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] Electrostatic forces
Berk Hess wrote: Hi Berk, Thanks for your feedback. I think there is still a general issue with optimizing the PME settings (or settings for any electrostatics method) for MD simulations. The question is what exactly one should optimize. If you do a single point calculation, you might only want to minimize the force error. But for MD you might also want good energy conservation. Optimizing the RMS force is certainly not the best choice, since that would lead to a large ewald_rtol, which gives small errors before the cut-off and on most of the long-range part, but large errors just beyond the cut-off. This will lead to bad energy conservation. Even an absolute force error will probably lead to a too large ewald_rtol. I think the optimization target function should be the RMS error over the 3 components of the total force on each of the N atoms. Thus the RMS is over 3N values. I can't see how this optimization process would seek an (rcoulomb, ewald_rtol) point where large errors at r = rcoulomb+delta exist, since this large error would propagate immediately to the error in the total force on each atom, and persist through the subsequent RMS averaging, since all atoms are affected similarly. If the RMS averaging was over all contributions to the components of the total force on each atom (which is not well-formed for Ewald anyway) then I could maybe see such a problem arising. I do agree that such an optimization should check for suitable energy conservation also. Someone planning NVE has different requirements from NVT, etc, and so they may need to optimize differently. Mark ___ 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: protein in SDS/water
Thomas Schlesier wrote: Hi, i think another problem lies here: ; Include water topology #include "spc.itp" . ; Include generic topology for ions #include "ions.itp" ; Include topology for SDS #include "SDS.itp" [ system ] ; Name Protein in water with SDS [ molecules ] ; Compound#mols Protein 1 SDS2000 SOL 36173 You have defined your Protein, then the water, then ions and then SDS. But in [ molecules ] you have the order Protein - SDS - water; but these two orders must be the same. -> Delete the line, which Justin suggested und put the *#include "SDS.itp"* before the *#include "spc.itp"*, then i think all must be fine. I believe this is not true. The order within [ molecules ] must match the ordering in the coordinate file supplied with this .top file to grompp. There would be no good reason to implement grompp such that it ignored the molecule type names and required the same ordering of the [ moleculetype ] sections as in [ molecules ] - lookup of string names would be much more robust and user-friendly. Mark ___ 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] covalent bond lookup table
Stefano Meliga wrote: Dear Gromacs users, I need to produce a list of the covalent bonds of my protein structure in the format: Atom1 Atom2 binding energy 12 50 kcal/mol 13 150 kcal/mol ... The binding energy is not the potential calculated by gromacs' force field but the diatomic binding energies available in the literature I actually already have a list of the covalent bonds like this Atom1 Atom2 12 13 ... and a table with the binding energies of each bond type like this bond type binding energy C-C 150 kcal/mol C=C 200 kcal/mol C-H 100 kcal/mol but, in order to create such file, I'd need to build a script that scans my pdb looking for the atom types and working out whether in between there's a single or double bond according to the aminoacid's chemical formula. Thus, I was wondering if Gromacs can perform any operation to make my work less painful. Is there a command or an option able to output a similar file? Not really. Forcefields select bonded interaction functions based on the types of the atoms involved. There's no explicit consideration of the formal "bond number", except inasmuch as some atom types never participate in double-bonding. sp2 carbons (tend to?) have different types from sp3 carbons. Perhaps you could infer the kind of bond from the atom types and/or the stiffness of the bonded potential. You would still have to have a script parse the atom types and bonds described in a .top file, look up the ff???bon.itp file and use that data to look up your own tables. You could also get the data from a script processing a gmxdump of a .tpr file. Mark It would be already of great help to have a simple lookup table like this Atom1 Atom2 single-or-double-bond? 12single 13double ... I took a quick look to the files ffoplsaa.* but I couldn't quite find what I was looking for. Maybe the field "name" of the *.itp file could be useful. Can you think of an easy solution? Thanks, Stefano ___ 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 ___ 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
[gmx-users] Re: protein in SDS/water
Dear all, thank you for continuous support. Here briefly what I made: 1) I deleted SDS from the first [moleculetype] section of the old .top file = doesn't work 2) I added a new [moleculetype] section after #include "ions.itp", followed by #include "SDS.itp" (just before [ system ] and [ molecule ] sections - I think it is "after the final subsection of any other [moleculetype] section" as Mark suggested) = doesn't work 3) In [ molecules ] section I changed the order Protein-SDS-SOL with Protein-SOL-SDS = doesn't work I really think I did all possible combination of attempts following your last suggestions...but GROMACS still claims that the number of coordinates in coordinate file does not match topology and the coordinates in .top file are 0. I'm copying here the last .top file I produced (and that doesn't work...). I kindly ask you to refer to this file for any further suggestions. Anna ; ; File 'my_prot.top' was generated ; By user: anna (62867) ; On host: bioserv1.isa.cnr.it ; At date: Tue Jun 16 16:15:08 2009 ; ; This is your topology file ; "The World is a Friendly Place" (Magnapop) ; ; Include forcefield parameters #include "ffG43a1.itp" [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 3 H 1SER H2 1 0.248 1.008 ; qtot 0.625 . . 2280 C229GLU C980 0.27 12.011 ; qtot -6.73 2281 OM229GLU O1980 -0.63515.9994 ; qtot -7.365 2282 OM229GLU O2980 -0.63515.9994 ; qtot -8 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_2 1 5 2gb_20 ... ... 2275 2276 2gb_26 2276 2277 2gb_26 2277 2278 2gb_5 2277 2279 2gb_5 2280 2281 2gb_5 2280 2282 2gb_5 [ pairs ] ; aiaj functc0c1c2c3 1 7 1 110 1 111 1 ... ... 2273 2275 1 2273 2280 1 2274 2277 1 2275 2278 1 2275 2279 1 2275 2281 1 2275 2282 1 2276 2280 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 2ga_9 2 1 4 2ga_9 2 1 5 2ga_10 3 1 4 2ga_9 3 1 5 2ga_10 . . 2275 2276 2277 2ga_14 2276 2277 2278 2ga_21 2276 2277 2279 2ga_21 2278 2277 2279 2ga_37 2274 2280 2281 2ga_21 2274 2280 2282 2ga_21 2281 2280 2282 2ga_37 [ dihedrals ] ; aiajakal functc0c1c2 c3c4 c5 2 1 5 9 1gd_14 1 5 6 7 1gd_17 1 5 911 1gd_20 5 6 7 8 1gd_12 5 91113 1gd_4 .. .. 2270 2272 2274 2280 1gd_19 2272 2274 2275 2276 1gd_17 2272 2274 2280 2282 1gd_20 2274 2275 2276 2277 1gd_17 2275 2276 2277 2279 1gd_20 [ dihedrals ] ; aiajakal functc0c1c2 c3 5 1 9 6 2gi_2 9 51110 2gi_1 11 91312 2gi_1 14131615 2gi_1 16141817 2gi_1 18162019 2gi_2 20182221 2gi_1 .. .. 2260 2256 2258 2261 2gi_1 2262 2249 2264 2263 2gi_1 2264 2262 2266 2265 2gi_1 2266 2264 2270 2267 2gi_2 2270 2266 2272 2271 2gi_1 2272 2270 2274 2273 2gi_1 2274 2272 2280 2275 2gi_2 2276 2279 2278 2277 2gi_1 2280 2274 2282 2281 2gi_1 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spc.itp
[gmx-users] RE: programmes to have in double precision besides mdrun_d
Thank you guys Indeed, it's better have all programmes in double version anyway. But now, I may be dreaming, but how 'impossible' is to have one single binary able to work with single or double precision with a simple input option or env variable? At least on Mac one can have more than one binary (for different archs) in 'single' file. And yes, a wrapping script could address that but it's not what I have in mind anyway. Cheers, Alan On Wed, Jun 17, 2009 at 15:16, wrote: >> Jussi Lehtola skrev: >> > On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote: >> > >> >> Hi, >> >> >> >> Nothing needs to be double precision. >> >> >> >> Why do you want mdrun in double precision? >> >> The only common reason for this is normal mode analysis, >> >> in which case you need all the tools involved in double precision. >> >> For normal MD simulation there is nearly never a need for >> >> double precision. >> >> >> > >> > If you want to run accurate NVE simulations, double precision is >> > important. If you use thermostats, then there is no need for double >> > precision. >> > >> > >> I can testify to that. Without double precision I've had problems with >> drifting total energy when doing non-periodic NVE. >> > > Indeed, this is correct. > But I guess this falls into the category nearly never. > On the other hand, there are so many Gromacs users nowadays, > there nearly never is nearly never zero users. > >> /Erik >> > Also, I have found that double precision can be nice for energy >> > minimization since it can handle more pathological cases than single >> > precision. Still, usually it doesn't matter much whether the starting >> > point was prepared in single or double precision. >> > > > > That's true. > It would be nice if we could make the single precision code > handle such cases better (force capping?). > > Berk > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< ___ 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: protein in SDS/water
Anna Marabotti wrote: [ moleculetype ] ; Name nrexcl SDS 3 ; Include topology for SDS #include "SDS.itp" Isn't this moleculetype already specified within SDS.itp? Perhaps posting the contents of SDS.itp will help solve this issue; the rest of the topology seems fine, except this section. [ system ] ; Name Protein in water with SDS [ molecules ] ; Compound#mols Protein 1 SOL 36173 SDS 2000 The [ molecules ] section must be in the same order as your coordinate file. -Justin I hope __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
[gmx-users] Re: Some questions about OPLS/Berger combination]
Hi Dorota, please keep all such correspondence on the gromacs mailing list. One can then send somebody a personal email indicating that you would appreciate it if they took a look. I have copied this answer to the list. Please respond there. Quoting Dorota Jamróz : Hallo Chris, While searching for information about a possibility to combine the Berger lipid FF with the OPLSA-AA I came across your posts at the gmx-users forum and also your text on the subject you made available on the net. I am a GROMACS beginner and I haven't yet mastered all the nuances of the program, which may be the reason of my problem, but I must admit I cannot understand the philosophy of your method. I would be very grateful if you could answer my questions and clear my doubts. To begin with - I presume, the main idea of the procedure is to modify the non-bonded parameters from the Berger FF so that the potential energy for the lipid, as calculated with the OPLS-AA formulas, gives the proper value (i.e same as it would be if calculated with Berger FF). Am I right on this point? Yes, as calculated with the OPLS-AA *1-4 rules* Next - I understand the main problem is the scaling of the 1-4 potential, which is 1 for Berger (i.e no scaling) and 0.5 for OPLS-AA (i.e. only half of the 1-4 potential is included into the total potential). If it is so then I would say, in order to get the proper 1-4 LJ potential you should either MULTIPLY the Berger epsilons by 2 or leave them as they are but insert a second copy of [ pairs ] into your topology file. Your solution was to DIVIDE the Berger epsilons by 2 AND include two [ pairs ] section. With the FudgeLJ = 0.5, as defined by OPLS-AA, the calculated LJ 1-4 potential will be then half of the proper value (taking half of the 1-4 LJ potential calculated with epsilons divided by 2 gives you 0.25 of the proper value. You sum these interaction twice, so finally you get the V(OPLS)=0.5V(Berger) ) The method is sound. A key realization is that the [ pairs ] section defines both the LJ and the Q pairs, so we will have double of each. We actually want double Q, since it was cut to 0.5 and 0.5*2=1.0. What we don't actually want is double epsilon, since the epsilon in question is already a special pairtypes epsilon that has been properly modified for 1-4 interactions. We thus cut epsilon in half to counteract the fact that we are forced to add it again twice in the pairs section. But don't take my word for it. Do a zero-step mdrun and look at your energy breakdown via g_energy for both lipid.itp/ffgmx and the hedp method. This is one of the things that I did to ensure that not only the idea was sound but there were not any unexpected bugs that would come to the surface with a double pairs list. Another point concerns the 1-4 Coulombic interaction; you state that dividing the Berger epsilons by 2 will modify both the 1-4 interactions types, the LJ and the Coulombic ones. I don't believe that I do say that anywhere. In what way will the Coulombic potential be changed? It does not depend on the epsilon value and, as I understand, there is no way to define another subset of charges for the 1-4 Coulomb interaction. The only way GROMACS allows you to modify this potential for specified pairs of atoms is to include it twice in the total potential, if a given pair is found in the [ pairs ] section. Summarizing, it seems to me that the 1-4 potential calculated with the parameters changed according to your method will give the right Coulombic potential but only half of the proper LJ potential. While I am always open to the possibility that I have made a mistake, I actually put a lot of time into developing this and distributing it, so I'm not very motivated to go look into it again before I see a bit of data or perhaps a proper mathematical derivation of whatever problem you propose. I still believe that the method is properly derived and implemented. Chris. As I wrote, it's pretty possible I am a victim to some misconception about how GROMACS works. In any case I would very grateful for you comment. Cheers, Dorota -- Dorota Jamróz, Ph.D Faculty of Chemistry Jagiellonian University ul.Ingardena 3, 30-060 Cracow, POLAND Phone: (+48) 012 6632263 e-mail: jam...@chemia.uj.edu.pl ___ 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
[gmx-users] Re: protein in SDS/water
Dear all, as requested, I'm copying here the SDS.itp file (it should be not too big): ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. [ moleculetype ] ; Name nrexcl SDS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 SDS O1S 1 -1.115 15.9994 2 SDMSO 1 SDS S 12.344 32.0600 3OM 1 SDS O3S 1 -1.114 15.9994 4OM 1 SDS O4 1 -1.115 15.9994 5OA 1 SDS O2S 2 -0.211 15.9994 6 CH2 1 SDS C1 20.053 14.0270 7 CH2 1 SDS C12 20.053 14.0270 8 CH2 1 SDS C11 20.052 14.0270 9 CH2 1 SDS C10 20.053 14.0270 10 CH2 1 SDS C9 30.000 14.0270 11 CH2 1 SDS C8 30.000 14.0270 12 CH2 1 SDS C7 30.000 14.0270 13 CH2 1 SDS C6 30.000 14.0270 14 CH2 1 SDS C5 30.000 14.0270 15 CH2 1 SDS C4 30.000 14.0270 16 CH2 1 SDS C3 30.000 14.0270 17 CH3 1 SDS C2 40.000 15.0350 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.153 804.00.153 804.0 ; S O1S 2 3 20.153 804.00.153 804.0 ; S O3S 2 4 20.153 804.00.153 804.0 ; S O4 2 5 20.153 804.00.153 804.0 ; S O2S 6 5 20.143 818.00.143 818.0 ;C1 O2S 6 7 20.153 715.00.153 715.0 ;C1 C12 7 8 20.153 715.00.153 715.0 ; C12 C11 8 9 20.153 715.00.153 715.0 ; C11 C10 9 10 20.153 715.00.153 715.0 ; C10 C9 10 11 20.153 715.00.153 715.0 ;C9 C8 11 12 20.153 715.00.153 715.0 ;C8 C7 12 13 20.153 715.00.153 715.0 ;C7 C6 13 14 20.153 715.00.153 715.0 ;C6 C5 14 15 20.153 715.00.153 715.0 ;C5 C4 15 16 20.153 715.00.153 715.0 ;C4 C3 16 17 20.153 715.00.153 715.0 ;C3 C2 [ pairs ] ; ai aj fuc0, c1, ... 1 6 1 ; O1S C1 2 7 1 ; S C12 3 6 1 ; O3S C1 4 6 1 ;O4 C1 5 8 1 ; O2S C11 6 9 1 ;C1 C10 7 10 1 ; C12 C9 8 11 1 ; C11 C8 9 12 1 ; C10 C7 10 13 1 ;C9 C6 11 14 1 ;C8 C5 12 15 1 ;C7 C4 13 16 1 ;C6 C3 14 17 1 ;C5 C2 [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2109.5 518.0109.5 518.0 ; O1SS O3S 1 2 4 2109.5 518.0109.5 518.0 ; O1SS O4 1 2 5 2109.5 518.0109.5 518.0 ; O1SS O2S 3 2 4 2109.5 518.0109.5 518.0 ; O3SS O4 3 2 5 2109.5 518.0109.5 518.0 ; O3SS O2S 4 2 5 2109.5 518.0109.5 518.0 ;O4S O2S 2 5 6 2120.0 530.0120.0 530.0 ; S O2S C1 5 6 7 2109.5 520.0109.5 520.0 ; O2S C1 C12 6 7 8 2109.5 520.0109.5 520.0 ;C1 C12 C11 7 8 9 2109.5 520.0109.5 520.0 ; C12 C11 C10 8 9 10 2109.5 520.0109.5 520.0 ; C11 C10 C9 9 10 11 2109.5 520.0109.5 520.0 ; C10 C9 C8 10 11 12 2109.
Re: [gmx-users] Re: protein in SDS/water
Anna Marabotti wrote: Dear all, as requested, I'm copying here the SDS.itp file (it should be not too big): ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. [ moleculetype ] ; Name nrexcl SDS 3 OK, as I thought, if you #include "SDS.itp" you should NOT specify a separate [moleculetype] directive in your system .top file. As I told sometimes ago, I obtained this file from PRODRG starting from a SDS.pdb file that I created using SDS coordinates found in another .pdb file (I simply copied and pasted the SDS coordinates in a new file and called it SDS.pdb). For my simulations, however, I used the SDS.gro file and SDS.itp file generated by PRODRG. I notice that the section [ moleculetype] is present in SDS.itp, but nothing changes if I erase the [ moleculetype ] section for SDS in my_prot.top: in all cases it doesn't work... I also copied and pasted the entire topology of SDS explicitly into my_prot.top instead of typing #include "SDS.itp", and nothing changed again... Well, the .itp file itself seems to have been properly generated. Concerning the order of molecules in the last [ molecules ] section, I changed it several times, and nothing changed... I'm still with an unclarified question: why genbox did not create by itself all corrections necessary to the original .top file when I used the -ci -nmol options? I added the -p flag but it doesn't change the topology by itself (as it should do, in my opinion). It would be nice if the computers did everything for us, wouldn't it? :) Maybe one day. It looks like automated updates only work for addition of water. Perhaps this can be a future improvement to genbox. Have you read the error page for your problem: http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology There is a specific section on the case where grompp detects 0 coordinates in the .top that might be relevant. -Justin Thank you again Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
[gmx-users] Free energy videos from EMBO course
Hello. I am trying to access the videos from EMBO course available in Gromacs' wiki but I can't have access to any of them. Are they available only for a strict community or something like that? I also would like some advice on how to perform a calculation of free-energy of dimerization between two protein helices in a membrane model. I have read some works saying that they've done it using PMF. The problem is that I do not have much expertise on the matter and need some advice on what to read and what would be the best way to get information (both theoretical and practical) on the matter. Thank you in advance Fabrício Bracht ___ 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
[gmx-users] Stop the simulation after a particular condition is fulfilled
hello, I want to stop my simulation in between after the density of system reaches 300kg/m3. Is there any possible way of doing this? Thank you. -- == Animesh Agarwal M.Tech(Integrated 5 yrs.)-Part III Industrial Chemisty Deptt. of Applied chemistry I.T B.H.U-Varanasi India == ___ 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
[gmx-users] The Cut-off for coulombtype heat up the water system?
Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] Stop the simulation after a particular condition is fulfilled
animesh agarwal wrote: hello, I want to stop my simulation in between after the density of system reaches 300kg/m3. Is there any possible way of doing this? Not in an automated fashion. Obviously, you will have to look (manually with g_energy) at a post-equilibration time-averaged density, not an instantaneous one or one over the whole simulation. Mark ___ 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] The Cut-off for coulombtype heat up the water system?
Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] mpi mdrun
Hi Mark! Thanks for the tip I got it the mpi mdrun running on my quad core machine. I just have one small clarification. In the output file md.log I see this message "Started mdrun at node (0)" I monitor my processor's load using gkrellm to see how many are running. When I started the mdrun ( mpirun -np 4 mdrun ) I specified 4 processors and gkrellm displays the four processors running to full capacity but why does the output in md.log give the above message. I am wondering if I missed out some thing !! Thanks JJ On Tue, Jun 16, 2009 at 2:47 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi !! >> I am attempting to install mpi mdrun such that I can use all four >> processors of my quad core system. But I keep running into this problem!! My >> operating system is Suse 10.1. >> >> (cd .libs && rm -f libgmxpreprocess_mpi.la < >> http://libgmxpreprocess_mpi.la> && ln -s ../libgmxpreprocess_mpi.la < >> http://libgmxpreprocess_mpi.la> libgmxpreprocess_mpi.la < >> http://libgmxpreprocess_mpi.la>) >> make[1]: *** No rule to make target `../mdlib/libmd_mpi.la < >> http://libmd_mpi.la>', needed by `mdrun'. Stop. >> make[1]: Leaving directory `/usr/local/gromacs-4.0.3/src/kernel' >> >> I would appreciate help/suggestions in my installation. >> > > Don't install in root filespace. Unpack the distribution in your own home > directory, configure, make, and then switch to root for "make install". > Also, why bother installing a version that's months old? > > Mark > ___ > 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 > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ 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
[gmx-users] x2top
hi gmx-users i was reading , in other post, the posibillity to run a new molecule without create new .rtp file , but when i run that program, he gives me the next error message Program x2top, VERSION 3.3.3 Source code file: ../../../../src/kernel/x2top.c, line: 206 Fatal error: Could only find a forcefield type for 654 out of 834 atoms i read that in this file http://oldwww.gromacs.org/pipermail/gmx-users/2006-September/024068.html I really apreciate your help best regards ___ 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] mpi mdrun
jayant james wrote: Hi Mark! Thanks for the tip I got it the mpi mdrun running on my quad core machine. I just have one small clarification. In the output file md.log I see this message "Started mdrun at node (0)" I monitor my processor's load using gkrellm to see how many are running. When I started the mdrun ( mpirun -np 4 mdrun ) I specified 4 processors and gkrellm displays the four processors running to full capacity but why does the output in md.log give the above message. I am wondering if I missed out some thing !! Well that's all fairly normal. The top of your .log file will indicate how many MPI processes are running. Mark ___ 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
[gmx-users] pulling molecule insert into DPPC lipid bilayer
Dear, gmx-users I can't pull molecule into DPPC lipid bilayer. I want file.mdp to use MD simulations. Please. From Wara ___ 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] pulling molecule insert into DPPC lipid bilayer
wara boon wrote: Dear, gmx-users I can't pull molecule into DPPC lipid bilayer. I want file.mdp to use MD simulations. Please. That won't fix your problems. If you need to learn, do some tutorials and read some documentation and try things out. Mark ___ 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] mpi mdrun
Hi! Oh!! I see that nnodes: 1. So does that mean that the job I gave is not running on four processors? If so how am I to solve this problem? thanks JJ On Wed, Jun 17, 2009 at 9:10 PM, Mark Abraham wrote: > jayant james wrote: > >> Hi Mark! >> Thanks for the tip I got it the mpi mdrun running on my quad core machine. >> I just have one small clarification. In the output file md.log I see this >> message >> >> "Started mdrun at node (0)" >> >> I monitor my processor's load using gkrellm to see how many are running. >> When I started the mdrun ( mpirun -np 4 mdrun ) I specified 4 processors >> and gkrellm displays the four processors running to full capacity but why >> does the output in md.log give the above message. I am wondering if I missed >> out some thing !! >> > > Well that's all fairly normal. The top of your .log file will indicate how > many MPI processes are running. > > > Mark > ___ > 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 > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ 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] mpi mdrun
jayant james wrote: Hi! Oh!! I see that nnodes: 1. So does that mean that the job I gave is not running on four processors? If so how am I to solve this problem? You haven't configured your MPI system with a suitable hostfile/whatever for your machine, probably. Mark ___ 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
[gmx-users] error pull MD
Hello, I pull molecule into membrane by MD simulations but it error about processing topology... Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxbon.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ff_dum.itp Generated 1284 of the 1485 non-bonded parameter combinations Opening library file /home/Ell/gromacMPI/share/gromacs/top/spc.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_C' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_D' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_E' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_F' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_G' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_H' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_I' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_J' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_K' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_L' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_M' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_N' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_O' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_P' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_Q' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_R' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_S' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_T' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_U' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_V' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_W' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_X' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_Y' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_Z' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'VIV' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 325 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /home/Ell/gromacMPI/share/gromacs/top/aminoacids.dat There are: 3784 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Pull group 0 'DPP' has 6400 atoms Pull group 1 'VIV' has 32 atoms Making dummy/rest group for Acceleration containing 17397 elements Making dummy/rest group for Freeze containing 17397 elements Making dummy/rest group for Energy Mon. containing 17397 elements Making dummy/rest group for VCM containing 17397 elements Number of degrees of freedom in T-Coupling group DPP is 12926.89 Number of degrees of freedom in T-Coupling group VIV is 62.99 Number of degrees of freedom in T-Coupling group SOL is 21928.12 Making dummy/rest group for User1 containing 17397 elements Making dummy/rest group for User2 containing 17397 elements Making dummy/rest group for XTC containing 17397 elements Making dummy/rest group for Or. Res. Fit containing 17397 elements Making dummy/rest group for QMMM containing 17397 elements T-Coupling has 3 element(s): DPP VIV SOL Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(
Re: [gmx-users] error pull MD
wara boon wrote: Hello, I pull molecule into membrane by MD simulations but it error about processing topology... Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxbon.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ff_dum.itp Generated 1284 of the 1485 non-bonded parameter combinations Opening library file /home/Ell/gromacMPI/share/gromacs/top/spc.itp Opening library file /home/Ell/gromacMPI/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_C' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_D' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_E' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_F' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_G' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_H' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_I' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_J' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_K' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_L' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_M' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_N' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_O' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_P' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_Q' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_R' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_S' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_T' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_U' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_V' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_W' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_X' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_Y' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_Z' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'VIV' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 325 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /home/Ell/gromacMPI/share/gromacs/top/aminoacids.dat There are: 3784 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Pull group 0 'DPP' has 6400 atoms Pull group 1 'VIV' has 32 atoms Making dummy/rest group for Acceleration containing 17397 elements Making dummy/rest group for Freeze containing 17397 elements Making dummy/rest group for Energy Mon. containing 17397 elements Making dummy/rest group for VCM containing 17397 elements Number of degrees of freedom in T-Coupling group DPP is 12926.89 Number of degrees of freedom in T-Coupling group VIV is 62.99 Number of degrees of freedom in T-Coupling group SOL is 21928.12 Making dummy/rest group for User1 containing 17397 elements Making dummy/rest group for User2 containing 17397 elements Making dummy/rest group for XTC containing 17397 elements Making dummy/rest group for Or. Res. Fit containing 17397 elements Making dummy/rest group for QMMM containing 17397 elements T-Coupling has 3 element(s): DPP VIV SOL Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC
