Re: [gmx-users] Free energy
The biotin-streptavidin interaction is on the order of -75 kJ/mol, so a binding free energy of -300 kJ/mol (dissociation constant of 10^-52 M) means something is fundamentally wrong - start by taking a hard look at your protocol, as convergence problems wouldn't account for that kind of deviation. From: mohsen ramezanpour ramezanpour.moh...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, 29 December, 2010 20:36:59 Subject: [gmx-users] Free energy Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? what is the range of correct value for a typical protein-ligand? protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error:Chain identifier
Dear Justin, Firstly, Thanks for your help. You said You're going from the end of chain B to the beginning of chain A, then back to B later on. Also realize that whatever ABSG or BSG is. How do you understand it? Where can I find such an important theoretical information? Thanks in advance 29 Aralık 2010 20:07 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: OK. if I do what sort change in pdb file, there is no need to create .rtp file. It seems difficult to create the .rtp file. That depends on whether you need this residue, hence all of my previous questions. If there is some functional significance to this residue and you need it for a simulation, then you'll either need to deal with the .rtp file, which actually is not terribly difficult, it just involves a little bit of reading and studying existing examples. Otherwise, if the molecule is non-covalently bound to the protein, follow the tutorial I linked before, and pay attention to the hint I gave you before about using PRODRG, which I will reiterate more explicitly: the output topology from PRODRG will require manual modification and validation. http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin Thanks for your help 29 Aralık 2010 19:49 tarihinde Justin A. Lemkul jalem...@vt.edu mailto: jalem...@vt.edu yazdı: ahmet yıldırım wrote: You said You do not have to make changes in pdb file. When did I say that? Then How will I create .rtp file. That depends entirely upon what that residue is. Is it a constituent residue of the protein, such that its backbone is incorporated in the protein structure? Is it connected via a sidechain? Or is it a ligand? Any or all of the following might apply: http://www.gromacs.org/Documentation/File_Formats/.rtp_File http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field http://www.gromacs.org/Documentation/File_Formats/specbond.dat http://www.gromacs.org/Documentation/Tutorials#General (Drug-enzyme complex, although beware the use of PRODRG) And, of course, the manual, which describes the contents of the .rtp file more thoroughly. -Justin 29 Aralık 2010 19:32 tarihinde Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Justin, Thanks for your reply. Where is the error? Pdb file: ATOM 1 N ALA A 4 ATOM 2 CA ALA A 4 ATOM 2688 N ALA B 4 ATOM 2689 CA ALA B 4 ATOM 5449 OXT GLN B 361 TER5450 GLN B 361 Right here. You're going from the end of chain B to the beginning of chain A, then back to B later on. Also realize that whatever ABSG or BSG is, it won't be recognized by pdb2gmx unless you've built a proper .rtp entry for it. -Justin HETATM 5451 OAAABSG A 1 HETATM 5452 OABABSG A 1 HETATM 5474 OAAABSG B 2 HETATM 5475 OABABSG B 2 HETATM 5492 O HOH A 2 HETATM 5493 O HOH A 362 HETATM 5494 O HOH A 363 HETATM 5744 O HOH B 362 HETATM 5745 O HOH B 363 29 Aralık 2010 19:12 tarihinde Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Mark, The chain identifier have continuous. In sequence does not show any problem. Then you're not looking at the right contents; pdb2gmx wouldn't complain otherwise. Usually HETATM entries like HOH (water) are after all protein chains, so you might have chains A, B, C, etc for protein followed by A, B, C, etc for water. Have a more thorough look through the .pdb file. -Justin 29 Aralık 2010 15:10 tarihinde Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
Re: [gmx-users] Desktop Freezes While Using mdrun-gpu
Hi Solomon, Just stumbled upon your mail and I thought you could still use a answer to your question. First of all, as you've probably read on the Gromacs-GPU page, a) you need a high-performance GPU to achieve good performance (in comparison to the CPU) -- that's the reason for the strict compatibility list and the warning about overriding this. Ideally, the Gromacs-GPU MD code should be able to run on every compute-capability-wise compatible GPU. However, it does not really make sense to use mobile or other lower-end GPUs. Moreover, I have seen freezes and extreme slowdowns when running on such hardware, especially if the graphics card is also used for display. Regarding your problem, I don't have an instant solution, but as I said, except for trying it out you won't gain much with the 330M chip. What OS are you using? Have you tried with the latest drivers and CUDA library? If you are using Linux, try to stop the X server and start the simulation in console mode. Cheers, -- Szilárd On Sat, Dec 4, 2010 at 7:17 PM, Solomon Berman smber...@bu.edu wrote: Hello friends, I'm writing today to see if anyone could offer further insight/commentary than the current available documentation and comments from the program itself concerning the following problem. I am currently using mdrun-gpu, v 4.5.3, utilizing my GPU, an NVIDIA GeForce GT 330M. When I run the program, my desktop freezes, though I am able to move my cursor about. I can hear the fan growing louder and the computer heating up, as it always does when I use the CPU mdrun. Browsing the available documentation, I recognize that my particular GPU is not listed as one of the tested. However, from reading further, and from the error codes generated by mdrun-gpu, I am suspect that it is possible to use a GPU not listed in the manual, so long as the other requirements (such as the use of the OpenMM library) are met. Could anyone who is using the GPU version perhaps offer some insight into what is occurring and any potential fixes that may be successful? I would be most appreciative? Also, if I haven't provided enough information, I'm more than happy to answer any questions quickly and succinctly to do so! Many thanks for any help anyone can provide! Best, Solomon Berman Department of Chemistry Boston University -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Antw: [gmx-users] NaN error using mdrun-gpu
Hi, I've never seen/had my hands on the Tesla T10 so I didn't know that's the name it reports. I'll fix this for the next release. Rest assured that on this hardware Gromacs-GPU should run just fine. On the other hand, your driver version is very strange: CUDA Driver Version = 4243455, while it should be 3.2. Are you sure your CUDA setup is not messed up? Do other programs run well? Cheers, -- Szilárd 2010/12/15 Bongkeun Kim b...@chem.ucsb.edu: Hello, This is the output from deviceQuery command: ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) There are 4 devices supporting CUDA Device 0: Tesla T10 Processor CUDA Driver Version: 3.20 CUDA Runtime Version: 3.20 CUDA Capability Major revision number: 1 CUDA Capability Minor revision number: 3 Total amount of global memory: 4294770688 bytes Number of multiprocessors: 30 Number of cores: 240 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 16384 bytes Total number of registers available per block: 16384 Warp size: 32 Maximum number of threads per block: 512 Maximum sizes of each dimension of a block: 512 x 512 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 256 bytes Clock rate: 1.44 GHz Concurrent copy and execution: Yes Run time limit on kernels: No Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Device 1: Tesla T10 Processor CUDA Driver Version: 3.20 CUDA Runtime Version: 3.20 CUDA Capability Major revision number: 1 CUDA Capability Minor revision number: 3 Total amount of global memory: 4294770688 bytes Number of multiprocessors: 30 Number of cores: 240 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 16384 bytes Total number of registers available per block: 16384 Warp size: 32 Maximum number of threads per block: 512 Maximum sizes of each dimension of a block: 512 x 512 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 256 bytes Clock rate: 1.44 GHz Concurrent copy and execution: Yes Run time limit on kernels: No Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Device 2: Tesla T10 Processor CUDA Driver Version: 3.20 CUDA Runtime Version: 3.20 CUDA Capability Major revision number: 1 CUDA Capability Minor revision number: 3 Total amount of global memory: 4294770688 bytes Number of multiprocessors: 30 Number of cores: 240 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 16384 bytes Total number of registers available per block: 16384 Warp size: 32 Maximum number of threads per block: 512 Maximum sizes of each dimension of a block: 512 x 512 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 256 bytes Clock rate: 1.44 GHz Concurrent copy and execution: Yes Run time limit on kernels: No Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Device 3: Tesla T10 Processor CUDA Driver Version: 3.20 CUDA Runtime Version: 3.20 CUDA Capability Major revision number: 1 CUDA Capability Minor revision number: 3 Total amount of global memory: 4294770688 bytes Number of multiprocessors:
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
Dear gromacs users My simulation system contains protein, dna, water molecules and Na+ ions respectively. I want to reorder water molecules with Na+ ions in final xtc file as at first 1-1867 complex (protein and dna) 1868 - 24085 SOL (water molecules) 24086 - 24099Na+ (ions) after reordering 1-1867 complex (protein and dna) 1868 -1881 Na+ (ions) 1882 - 24099 SOL (water molecules) How to do that? I need to this reordering to obtain amber trajectory file (mdcrd) by VMD. any help and suggestion will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
Dear Leila:
Perhaps I took the long way around, but I am not aware of any such
tool. You can make custom modifications to things like trjconv as
follows.
!!! Please note: I didn't test this except to see that it compiles.
You should run some analyses before and after switching the order to
check that the file hasn't been corrupted.
This is done with gromacs 4.0.7.
cd src/tools
cp gmx_trjconv.c ../../exec/share/gromacs/template/my_tool.c
### Add the following text to the bottom of the my_tool.c file:
int
main(int argc,char *argv[])
{
return gmx_trjconv(argc,argv);
}
### Now go to line 1246 of the file and replace this:
for(i=0; inout; i++) {
copy_rvec(fr.x[index[i]],frout.x[i]);
if (bVels fr.bV) {
copy_rvec(fr.v[index[i]],frout.v[i]);
}
if (bForce fr.bF) {
copy_rvec(fr.f[index[i]],frout.f[i]);
}
}
### with this:
for(i=0; i=1866; i++) {
copy_rvec(fr.x[index[i]],frout.x[i]);
}
for(i=24085; i=24098; i++) {
copy_rvec(fr.x[index[i]],frout.x[i-22218]);
}
for(i=1867; i=24084; i++) {
copy_rvec(fr.x[index[i]],frout.x[i+14]);
}
for(i=0; inout; i++) {
if (bVels fr.bV) {
copy_rvec(fr.v[index[i]],frout.v[i]);
}
if (bForce fr.bF) {
copy_rvec(fr.f[index[i]],frout.f[i]);
}
}
}
### That's not going to modify the forces and velocities, but I
assume that this will be ok for you. If you need them, you can add
that part by analogy.
### Now create the makefile:
sed s/template/my_tool/g Makefile.x86_64-unknown-linux-gnu
Makefile.my_tool
### now compile it:
make -f Makefile.my_tool
-- original message --
Dear gromacs users
My simulation system contains protein, dna, water molecules and Na+
ions respectively.
I want to reorder water molecules with Na+ ions in final xtc file as
at first
1-1867 complex (protein and dna)
1868 - 24085 SOL (water molecules)
24086 - 24099Na+ (ions)
after reordering
1-1867 complex (protein and dna)
1868 -1881 Na+ (ions)
1882 - 24099 SOL (water molecules)
How to do that?
I need to this reordering to obtain amber trajectory file (mdcrd) by VMD.
any help and suggestion will highly appreciated.
--
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Add gromacs forcefield w/ virtual site
Thank you Chris for your answer: 1) The molecule has no net charge because the virtual site in the center of mass is a point charge twice the charge in the O atom. 2) Until now I've created 5 files but I don't know if I am doing the right thing: * forcefield.itp #define _FF_OXY [ defaults ] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 12no 1.01.0 #include ffnonbonded.itp #include ffbonded.itp *ffbonded.itp [ bondtypes ] ; ij func OO 5 (I've used function 5 because the forcefield has a fixed length, is it right?) ; *ffnonbonded.itp [ atomtypes ] ; name at.nummass charge ptype sigma epsilon O8 15.99940-0.123 A 3.01300e-014.0780822e-01 COM0 0.00 0.246 V 0.0e+000.000e+00 * atomtypes.atp O 15.99940 ; Oxygen Atom COM 0.0 ; Virtual site (COM charge) * residues.rtp ; Oxygen [ OXY ] [ atoms ] O O -0.1231 COM COM0.2461 [ bonds ] OO 3) Is it necessary more or less files? And in which file do I specificate de virtual site? 4) The virtual site in the COM is [ virtual_sites2 ] with a = 0.5 or [ virtual_sitesn ]? Thank you again for your time. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Major code reorganization in git coming up
Hi! We figured we'd celebrate the upcoming new year with some major changes in the git development branch, consisting primarily of C++ support and a more modular organization of files. This is a gradual process, so this mail is a bit of a warning-message that the master/development branch might have some issues with compilers/build environments the next couple of weeks. If you occasionally use a git build to run production simulation, just use the release-4-5-patches branch instead, and everything should be fine. However, If you are working on your own code based on the git master branch, it might be a good idea to either switch to the release-4-5-patches branch, or create your own branch that you no longer sync with master as frequently. In the latter case you might have to go through some pain to port your code back to the new file organization later (sorry about that). The upside of all this is that the file organization will gradually get easier to understand, and the code itself should also get much more modular and readable (which we hope will lead to a faster release schedule and more features :-) Happy new year! Erik -- Erik Lindahl e...@kth.se Professor of Theoretical Computational Biophysics Department of Theoretical Physics Swedish e-Science Research Center Royal Institute of Technology, Stockholm, Sweden Tel: +46855378029 Cell: +46703844534 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Major code reorganization in git coming up
Hi! We figured we'd celebrate the upcoming new year with some major changes in the git development branch, consisting primarily of C++ support and a more modular organization of files. This is a gradual process, so this mail is a bit of a warning-message that the master/development branch might have some issues with compilers/build environments the next couple of weeks. If you occasionally use a git build to run production simulation, just use the release-4-5-patches branch instead, and everything should be fine. However, If you are working on your own code based on the git master branch, it might be a good idea to either switch to the release-4-5-patches branch, or create your own branch that you no longer sync with master as frequently. In the latter case you might have to go through some pain to port your code back to the new file organization later (sorry about that). The upside of all this is that the file organization will gradually get easier to understand, and the code itself should also get much more modular and readable (which we hope will lead to a faster release schedule and more features :-) Happy new year! Erik -- Erik Lindahl e...@kth.se Professor of Theoretical Computational Biophysics Department of Theoretical Physics Swedish e-Science Research Center Royal Institute of Technology, Stockholm, Sweden Tel: +46855378029 Cell: +46703844534 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Add gromacs forcefield w/ virtual site
Sorry Marcelo, that sounds like a job for an author ;) If nobody else chimes in, then I suggest that you do some testing and come back to the list with specific problems. As an analogy, you might look at how the virtual site is handled in tip4p in the absence of settle. Chris. -- original message -- Thank you Chris for your answer: 1) The molecule has no net charge because the virtual site in the center of mass is a point charge twice the charge in the O atom. 2) Until now I've created 5 files but I don't know if I am doing the right thing: * forcefield.itp #define _FF_OXY [ defaults ] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 12no 1.01.0 #include ffnonbonded.itp #include ffbonded.itp *ffbonded.itp [ bondtypes ] ; ij func OO 5 (I've used function 5 because the forcefield has a fixed length, is it right?) ; *ffnonbonded.itp [ atomtypes ] ; name at.nummass charge ptype sigma epsilon O8 15.99940-0.123 A 3.01300e-014.0780822e-01 COM0 0.00 0.246 V 0.0e+000.000e+00 * atomtypes.atp O 15.99940 ; Oxygen Atom COM 0.0 ; Virtual site (COM charge) * residues.rtp ; Oxygen [ OXY ] [ atoms ] O O -0.1231 COM COM0.2461 [ bonds ] OO 3) Is it necessary more or less files? And in which file do I specificate de virtual site? 4) The virtual site in the COM is [ virtual_sites2 ] with a = 0.5 or [ virtual_sitesn ]? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_tune_pme big standard deviation in perf.out output
Dear GMXers, I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The command g_tune_pme was used to find the optimal PME node numbers, Coulomb cutoff radius and grid spacing size. The following command is used: g_tune_pme -np 24 -steps 5000 -resetstep 500 ... rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The simulation is done with no error. Below is the output: --- Line tpr PME nodes Gcycles Av. Std.dev. ns/dayPME/fDD grid 0 0 12 2813.762 187.1159.6040.361 4 3 1 1 0 11 2969.826 251.2109.1120.510 13 1 1 2 0 10 2373.469 154.005 11.3850.445 2 7 1 3 09 2129.519 58.132 12.6650.601 5 3 1 4 08 2411.653 265.233 11.2480.570 4 4 1 5 07 2062.770 514.023 13.4900.616 17 1 1 6 06 1539.237 89.189 17.5470.748 6 3 1 7 00 1633.318 113.037 16.548 - 6 4 1 8 0 -1( 4) 1330.146 32.362 20.2761.050 4 5 1 --- The optimal -npme is 4. It seems to me that the Std. dev is too huge. Can anyone tell me the meaning of Gcycles Av. and Std. dev and their relations to the accuracy of ns/day? Another question: I tried g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of g_tune_pme) rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The optimal -npme is 6, different from -npme=4 as obtained with big -nsteps. Should I increase -nsteps even more to get better estimate, or what else parameters should I try? Do let me know if the questions are not made clear. Thank you. Best, Yanbin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Add gromacs forcefield w/ virtual site
On 31/12/2010 5:03 AM, Marcelo Silva wrote: Thank you Chris for your answer: 1) The molecule has no net charge because the virtual site in the center of mass is a point charge twice the charge in the O atom. 2) Until now I've created 5 files but I don't know if I am doing the right thing: * forcefield.itp #define _FF_OXY [ defaults ] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 12no 1.01.0 #include ffnonbonded.itp #include ffbonded.itp * ffbonded.itp [ bondtypes ] ; ij func OO 5 (I've used function 5 because the forcefield has a fixed length, is it right?) ; If the bond length is to be fixed, then you want constraint type 1. Bond type 5 has a different application. * ffnonbonded.itp [ atomtypes ] ; name at.nummass charge ptype sigma epsilon O8 15.99940-0.123 A 3.01300e-014.0780822e-01 COM0 0.00 0.246 V 0.0e+000.000e+00 * atomtypes.atp O 15.99940 ; Oxygen Atom COM 0.0 ; Virtual site (COM charge) * residues.rtp ; Oxygen [ OXY ] [ atoms ] O O -0.1231 COM COM0.2461 [ bonds ] OO 3) Is it necessary more or less files? And in which file do I specificate de virtual site? Virtual site directives are listed in Table 5.6, so they need to end up in the [moleculetype], which means they need to be in the .rtp entry. Some of the forcefield files probably have examples of this. 4) The virtual site in the COM is [ virtual_sites2 ] with a = 0.5 or [ virtual_sitesn ]? I guess either would work, but the former is simpler. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
