Re: [gmx-users] Error while running InflateGRO File
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I generated small molecule topology file from SwissParam which provides .pdb file for ligand molecule. I don't have .gro file for small molecule thats why I have created all the file in .pdb file format. when I run: perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat it gives error : Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... How to work with .pdb file to run inflategro.pl command?? can anyone please help me out how to solve this error. Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers
Is there a specific reason why you're not adding the water using genbox and genion? If that's not the case you can simply delete the waters from the pdb and only convert the rest of the system. Then you can solvate, set your box boundaries and add ions. Best, João *Joao Martins* joaomartins...@gmail.com On Tue, Aug 5, 2014 at 6:09 AM, WH signoreguid...@163.com wrote: Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance of beowulf cluster
On 05.08.2014 07:01, Abhishek Acharya wrote: I am planning on investing in a beowulf cluster with 6 nodes (48 cores) each with AMD Fx 8350 processor, 8 GB memory connected by 1 Gigabit Ethernet switch. Although I plan to add more cores to this cluster later on, what is the max performance expected from the current specs for a 100,000 atom simulation box ? Also, is it better to invest in a single 48 core server ? The cluster system can be set up at almost half the price of a 48 core server, but do we lose out on performance in the process? 6 AMD-8350 boxes, connected to *one* 1GB switch? This system could be put to very good use if you are able to perform 6 *independent simulations* on your molecular system. 100,000 Atoms is a rather small system for large scale parallelization. A 100K SPC box would have an edge length of about 10nm? If it's important for you to have parallel runs on single molecular systems, you could consider a dual-socket-2011 system running 6-core i7 processors (i7/4930K or upcoming Haswell-E 5930K) combined with quad-channel DDR3/4. This would give you a 24x parallelization on a single workstation. What about modern (Nvidia) consumer graphics cards? These are supported very well by Gromacs. Regards M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Why is there a NxN VdW [F] on a separate line?
This is extracted from a log file of a mdrun of 512 openMP threads without GPU acceleration. Since the first line and third line both have N*N Vdw [F], does the former include the latter? As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella Sampling - no PMF plateau
Dear Gmx Users, I run US simulations between 2 nanotubes with attached proteins with distance as a reaction coordinate. This is a coarse-grain simulation, both tubes are placed across pbc so infinite in length. I have tabulated potentials for both bonded and non-bonded interactions. I observed that even at large distances between them in US windows when they do not interact (even across pbc) the PMF is still increasing... no plateau is observed... I tried it in many systems increasing the box size but still the same happening. The perido image is 15 nm away and the cutoff in potentials is 2 nm... Would you please advise? May that correspond to position restraint dynamics of tube atoms of one of them (from which I pulled the other one)? Or maybe tabulated potentials used? Steven -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error when trying to continue a simulation
Hi all, Can someone please help me with continuing a simulation. I did a 150 ns simulation and wanted to set up a test extension by 100 ps. I used the following commands and got some error messages tpbconv_mpi -s md.tpr -extend 100 -o next.tpr and mpirun -np 32 mdrun_mpi -s next.tpr -cpi md.cpt but I get the following error --- Fatal error: File appending requested, but only 1 of the 4 output files are present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- So I used the following commands tpbconv_mpi -s md.tpr -f md.trr -e md.edr -extend 100 -o next.tpr and mpirun -np 32 mdrun_mpi -s next.tpr -cpi md.cpt but keep getting the same error. Can someone please let me know what I'm doing wrong. I'd like to eventually extend the simulation by 50 ns. Thanks for your help. Kind regards, Sid. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] charged uncharged ligand
Dear gromacs users. My system contains protein + ligand. Total charge of my protein = 0 My ligand has -NH2 group. I want to do 2 md simulations: 1)deprotonated state of ligand (-NH2). = Total charge of system= 0 2)protonated state of ligand and (-NH3+)= Total charge of system=+1 I have no problem about the first simulation. I have a question about the second simulation: Should I one Cl ion to system using genion tool? I want to study effect of the charged ligand on the protein. Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance of beowulf cluster
Hi, You need fast network to parallelize across multiple nodes. 1 Gb ethernet won't work well and even even 10/40 Gb ethernet needs to be of good quality; you'd likely need to buy separate adapters, the on-board ones won't perform well. I posted some links to the list related to this a fed days ago. The AMD FX dekstop hardware you mention is OK, but I'm not sure that it's gives the best performance/price. If you find (very) discounted Sandy Bridge-E (i7 3930K) or the cheaper Haswells like i5 4670 may actually provide better prerformance for the money. Ivy Bridge-E or Haswell-E as Mirco suggests are the best single-socket workstation options, but those are/will be pretty expensive. Finally, unless you have a good reason not to, you should not just consider GPUs, but consider what CPU/platform works best with GPUs. Cheers, -- Szilárd On Tue, Aug 5, 2014 at 7:01 AM, Abhishek Acharya abhi117acha...@gmail.com wrote: Hello gromacs users, I am planning on investing in a beowulf cluster with 6 nodes (48 cores) each with AMD Fx 8350 processor, 8 GB memory connected by 1 Gigabit Ethernet switch. Although I plan to add more cores to this cluster later on, what is the max performance expected from the current specs for a 100,000 atom simulation box ? Also, is it better to invest in a single 48 core server ? The cluster system can be set up at almost half the price of a 48 core server, but do we lose out on performance in the process?? Regards, Abhishek Acharya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein simulation including ligand with Fe(III)
Hi Justin, Thank you for your answer. I was going to use the parameters from an MM paper but since you mentioned that, any idea where I can find some better parameters? I don't want them to be perfect and I don't have time for QM, just something so the protein won't blow up up. Thanks, Nicholas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] treatment of electrostatics in vaccum
Hi I need to run MD of a charged macromolecule in gas-phase or in vaccum. I was wondering if I use no periodic boundary condition ( i.e. setting pbc=no and ns_type=simple), can I get away with non-ewald type electrostatics method ( i.e. by using a very large cut-off like 3 or 4 nm for electrostatics ) ? In this case, I wanted to minimize the computing expense associated with PME electrostatics. Thanks Sanku -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?
On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si sjyz...@gmail.com wrote: This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. Since the first line and third line both have N*N Vdw [F], does the former include the latter? No, but there is no line with N*N Vdw [F]. Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers
In addition to what Joao said, the fixed-width .pdb format is fundamentally unsuited to large systems. You need to find a way to avoid using such a .pdb file as input to pdb2gmx; either solvate later, or use a different format for input. Mark On Mon, Aug 4, 2014 at 11:09 PM, WH signoreguid...@163.com wrote: Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a gromacs feature to do TMD like simulation
Dear Mr.Shahriyari , I have this problem too let me know plz, if u solve ur problem with gromacs... best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella Sampling - no PMF plateau
Hi Steven, I've run into a similar issue with CG simulations using tabulated potentials. For my system it turns out the continuous increase in PMF was due to the system freezing for some unknown reason. Once I annealed the system (~500 K) and messed around with the temperature coupling, the system unfroze, and I was eventually able to obtain the correct plateau in the PMF curve. Have you checked some of your configurations to see whether your system shows unphysical ordering? (I am assuming you are using an explicit solvent.) Hope this helps, Brian On Tue, Aug 5, 2014 at 5:19 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I run US simulations between 2 nanotubes with attached proteins with distance as a reaction coordinate. This is a coarse-grain simulation, both tubes are placed across pbc so infinite in length. I have tabulated potentials for both bonded and non-bonded interactions. I observed that even at large distances between them in US windows when they do not interact (even across pbc) the PMF is still increasing... no plateau is observed... I tried it in many systems increasing the box size but still the same happening. The perido image is 15 nm away and the cutoff in potentials is 2 nm... Would you please advise? May that correspond to position restraint dynamics of tube atoms of one of them (from which I pulled the other one)? Or maybe tabulated potentials used? Steven -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error with tabulated potential and tip4p water model
Thank you mark for the reply. But here i have only one polymer which i used optimized structure polymer and used genbox to generate box of solvent which obviously puts the water at different lattice points. It was never a problem to simulate when I was using the LJ potential. So, my concern here is about how the gromacs reads the table internally. So far, in the table, what I did is; I made all f,f',h,h' columns zero and calculated the total (sum of electrostatics+LJ/Buckingham+user defined potential) potential and put in the column g and the negative derivative of g in g' column thereby putting all the coefficients as 1 in the .itp file. When I try to use that table it gives me the warning that the derivative(-force) deviates from the potential by 164%(one example). While reading the Manual, I found that it uses the Cubic splines Algorithm to regenerate the table internally. I am not sure if that algorithm was not compatible with the way i created the table(for potential) or it is something else. Looks like I am lost somewhere in between here because EM was never a great problem until I used the tabulated potential. Udaya On Tue, Aug 5, 2014 at 10:38 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Generating a sane starting structure is not really in GROMACS problem space. You should take steps to ensure atoms are not closer to each other than is physically reasonable, and probably start with the coordinates of each molecule whole with respect to PBC. Start with a single polymer solvated, then perhaps use genconf to add complexity. Mark On Mon, Aug 4, 2014 at 8:48 AM, Udaya Dahal dahal.ud...@gmail.com wrote: It was immediate. But I figured out the way to solve that issue. Looks like the starting initial configuration was not so good. A different starting structure at least gave me the energy minimization to few steps but I kind of really find very hard to have the energy minimized to smaller value. The maximum force on the particular atom is around ...+03. Do I really have to amend each and every atom step by step(which still doesn't solve the problem) or there is any other specific way that we can get more/less energy minimized structure. Thank you for your help. On Sun, Aug 3, 2014 at 9:23 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Immediately, or after some EM steps? Mark On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal dahal.ud...@gmail.com wrote: I have tabulated potential for all the possible combinations(non bonded). I am using Tip4p water model for the polymer water interaction. While running the energy minimization i got the error like below. Fatal error: Settle block crossing node boundaries constraint between atoms 664, 665, 666) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any idea to slove this issue.? Thank you, Udaya. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Udaya Dahal, Graduate Assistant, Department of Physics, University of Connecticut -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
Re: [gmx-users] Performance of beowulf cluster
Thank you Mirco and Szilard, With regards to the GPU system, I have decided on a Xeon E5-1650 v2 system with GEForce GTX -780 Ti GPU for equilibration and production runs with small systems. But for large systems or REMD simulations, I am a bit skeptical on banking on GPU systems. Any pointers as to what would be the minimum configuration required for REMD simulations on say a 50 K atom protein sampled for 100 different temperatures? I am open to all possible options in this regard (obviously a little cost effectiveness does not harm ). Also, would investing in a *good* 40 Gigabit ethernet network ensure good performance if we later plan to more nodes to the cluster. Regards, Abhishek On Tue, Aug 5, 2014 at 5:46 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, You need fast network to parallelize across multiple nodes. 1 Gb ethernet won't work well and even even 10/40 Gb ethernet needs to be of good quality; you'd likely need to buy separate adapters, the on-board ones won't perform well. I posted some links to the list related to this a fed days ago. The AMD FX dekstop hardware you mention is OK, but I'm not sure that it's gives the best performance/price. If you find (very) discounted Sandy Bridge-E (i7 3930K) or the cheaper Haswells like i5 4670 may actually provide better prerformance for the money. Ivy Bridge-E or Haswell-E as Mirco suggests are the best single-socket workstation options, but those are/will be pretty expensive. Finally, unless you have a good reason not to, you should not just consider GPUs, but consider what CPU/platform works best with GPUs. Cheers, -- Szilárd On Tue, Aug 5, 2014 at 7:01 AM, Abhishek Acharya abhi117acha...@gmail.com wrote: Hello gromacs users, I am planning on investing in a beowulf cluster with 6 nodes (48 cores) each with AMD Fx 8350 processor, 8 GB memory connected by 1 Gigabit Ethernet switch. Although I plan to add more cores to this cluster later on, what is the max performance expected from the current specs for a 100,000 atom simulation box ? Also, is it better to invest in a single 48 core server ? The cluster system can be set up at almost half the price of a 48 core server, but do we lose out on performance in the process?? Regards, Abhishek Acharya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhishek Acharya Senior Research Fellow Gene Regulation Laboratory National Institute of Immunology -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] treatment of electrostatics in vaccum
On 8/5/14, 7:39 AM, Sanku M wrote: Hi I need to run MD of a charged macromolecule in gas-phase or in vaccum. I was wondering if I use no periodic boundary condition ( i.e. setting pbc=no and ns_type=simple), can I get away with non-ewald type electrostatics method ( i.e. by using a very large cut-off like 3 or 4 nm for electrostatics ) ? In this case, I wanted to minimize the computing expense associated with PME electrostatics. Infinite cutoffs would be more common. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cluster size and aggregation number calculation
On 8/5/14, 10:18 AM, Praveen Kumar wrote: Hi, I am new to Gromacs. Can anybody help me to tell how to calculate cluster size and aggregation number in a liquid? Try g_clustsize. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cluster size and aggregation number calculation
Hi, I am new to Gromacs. Can anybody help me to tell how to calculate cluster size and aggregation number in a liquid? Thanks Praveen -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error while running InflateGRO File
On 8/4/14, 11:53 PM, neha bharti wrote: Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I generated small molecule topology file from SwissParam which provides .pdb file for ligand molecule. I don't have .gro file for small molecule thats why I have created all the file in .pdb file format. when I run: perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat it gives error : Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... How to work with .pdb file to run inflategro.pl command?? can anyone please help me out how to solve this error. I answered this yesterday. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of Glass Surfaces?
Additionally, what is the difference between the different wall types? They are stated as 9-3, 10-4, and 12-6, but I don't know what is meant by that. On Tue, Aug 5, 2014 at 1:20 PM, AJ Lanphere ajlanph...@gmail.com wrote: So, I've been looking over the sections on walls in the manual and I have a few questions on the specifics. - Do the walls have to be composed of a solid material, or can they be set as just a boundary? I don't want my glass drifting out of the simulation box and into space, but I don't want it interacting with an interface, either. - Is it possible to remove periodicity from positive Z, but not negative Z? As in, can I set it up so that I'm only forming an exposed surface on one face of my box, instead of creating effectively a sheet of glass? I'm concerned that, since my simulation box is only 4.5nm on a side, creating two surfaces that close together will result in unrealistic structure. Thanks, AJ L On Mon, Jul 21, 2014 at 2:35 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-07-21 18:33, AJ Lanphere wrote: Hello all, I am using GROMACS to simulate the melting and annealing of glasses. Currently I've been working only with simulations of the glass bulk, with periodic boundaries so the glass is connected on all sides. I was wondering if GROMACS can be used to simulate solid surfaces, because I have not seen any methods for doing so in the manual and a brief literature search has also not returned any useful references. We have done some stuff with glass surfaces: David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 (2006) you can also use analytic walls, check the manual. Any advice would be greatly appreciated. Regards, AJ Lanphere Graduate Student Researcher Inamori School of Engineering, Alfred University 1 Saxon Drive, Alfred, NY 14802 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: k.sunny wants to share a link | Gromacs
k.sunny says: For phosphene (black phosphorus) which force field is useful in gromacs --- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] New residue in FF does not bond to others.
Dear Gromacs experts, I have found out why my force field does not work properly. I have added a new residue according to manual I found on Gromacs website. I modified all of the files. Now I have revealed that my new residue does not have connection to natural aminoacids in my topology file! If you take a look at it you will see that atoms 970 and 1009 are connected while the truth is that atoms 970 (carbonyl C atom of Phe65) and 1008 (MN1 atom of CH6 (new) residue) but also atoms 994 (MC3 atom of new residue) and 1009 (peptide N atom of Ser69) should be bonded. I have specified bonded parameters between those atom types in ffbonded.itp file but not in aminoacids.rtp. In other words my topology file does not recognize the connection between new residue and natural aminoacids residues. It seems like I do not specify something correctly in force field but I cannot find my mistake. Shall I specify this connection in specbond.dat file? Best wishes, Dawid Grabarek PS Here you will find all relevant files (I guess and I hope so :) ) but if you need sth more, please give me a shout: http://www.speedyshare.com/Dk2tu/charmm27-files.tar.bz2 http://www.speedyshare.com/vtePQ/mCherry7.tar.bz2 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of Glass Surfaces?
On 8/5/14, 11:20 AM, AJ Lanphere wrote: So, I've been looking over the sections on walls in the manual and I have a few questions on the specifics. - Do the walls have to be composed of a solid material, or can they be set as just a boundary? I don't want my glass drifting out of the simulation box and into space, but I don't want it interacting with an interface, either. Probably a flat-bottom potential (reflective boundary) is more along the lines of what you want. - Is it possible to remove periodicity from positive Z, but not negative Z? As in, can I set it up so that I'm only forming an exposed surface on one face of my box, instead of creating effectively a sheet of glass? I'm concerned that, since my simulation box is only 4.5nm on a side, creating two surfaces that close together will result in unrealistic structure. AFAIK, no, you can't manipulate periodicity in this way. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GBSA + infinite cutoff + GPU in GMX5?
Hi Based on the documentation ( http://www.gromacs.org/Documentation/Cut-off_schemes), it seems that, with GMX 5, GBSA implicit solvent simulations with infinite cutoff (rcoulomb = 0, rvdw = 0, pbc = no) cannot be done on GPUs. Is that right? For CPU simulations I am quite happy with 4.6.5! Best Sandeep -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Normalization In RDF, GROMACS
Hello Dear User, I am confused about the normalization in the g_rdf command. It should be noted that I understand the meaning of RDF but am not sure about the definition of RDF in GROMACS in detail. When I calculate the rdf of Hydrogen (HW) of water molecules around one Oxygen (OW) of one water molecule, I do not want the normalized option, and thus I use the -nonorm in g_rdf, which indicate that no Normalization is conducted for volume and density. I checked the results, namely the HW number distribution at different radical distances (R), the minimum value is 500, which is quite impossible. What the meaning of these value? Are these value means the HW numbers at different radical distance ? Additionally, all HW numbers are integral times of 500. In order to confirm this result, I normalize the data myself: dividing these values by the volume of the shell layer (4*pi*R^2*dl) and the average water density (33.4 N/nm^3). However, these calculated results is several order higher than the normalized results by Gromacs with default -norm option. Thanks in advance. Haiyang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Restrain the COM of a group of atoms
Hi All, I'm calculating the PMF of pulling a surfactant molecule from a polymer slab in aqueous phase. Therefore, my pull group is the surfactant and the reference group is the slab. To prevent the reference group (slab) from being dragged by the pull group (surfactant), I would like to restrain the COM of my reference group. I did this by removing the COM motion of my reference group using comm_grps mdp options. In addition, I also removed the COM motion of other atoms, including waters and ions in the system so that there are no external forces applying to the system. Therefore, I have two comm_grps: slab Waters and ion. As you may notice, my comm_grps does not include the pull group (surfactant), which triggers a warning by grompp, saying Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. I could have included the surfactant in the group of waters and ions but the fact that this surfactant is moving by an umbrella potential refrains me from doing so. My question is: 1. Does this seem to be a reasonable choice to restrain the COM of a reference group? 2. I have two groups in the removal of COM motion. Does this suggest I should also use the same two groups for temperature coupling? 3. For a MD step using a leapfrog algorithm, when does the COM removal happen? Does it occur after applying corrections due to constraints and before re-scaling the coordinates and box due to pressure coupling? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New residue in FF does not bond to others.
On 8/5/14, 11:59 AM, Dawid das wrote: Dear Gromacs experts, I have found out why my force field does not work properly. I have added a new residue according to manual I found on Gromacs website. I modified all of the files. Now I have revealed that my new residue does not have connection to natural aminoacids in my topology file! If you take a look at it you will see that atoms 970 and 1009 are connected while the truth is that atoms 970 (carbonyl C atom of Phe65) and 1008 (MN1 atom of CH6 (new) residue) but also atoms 994 (MC3 atom of new residue) and 1009 (peptide N atom of Ser69) should be bonded. I have specified bonded parameters between those atom types in ffbonded.itp file but not in aminoacids.rtp. In other words my topology file does not recognize the connection between new residue and natural aminoacids residues. It seems like I do not specify something correctly in force field but I cannot find my mistake. Shall I specify this connection in specbond.dat file? You don't need specbond.dat. If CH6 is connected within the peptide backbone, you need to specify bonds in the .rtp file to the previous and next residues with -/+ and appropriate atom names. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New residue in FF does not bond to others.
On 8/5/14, 11:59 AM, Dawid das wrote: Dear Gromacs experts, I have found out why my force field does not work properly. I have added a new residue according to manual I found on Gromacs website. I modified all of the files. Now I have revealed that my new residue does not have connection to natural aminoacids in my topology file! If you take a look at it you will see that atoms 970 and 1009 are connected while the truth is that atoms 970 (carbonyl C atom of Phe65) and 1008 (MN1 atom of CH6 (new) residue) but also atoms 994 (MC3 atom of new residue) and 1009 (peptide N atom of Ser69) should be bonded. I have specified bonded parameters between those atom types in ffbonded.itp file but not in aminoacids.rtp. In other words my topology file does not recognize the connection between new residue and natural aminoacids residues. It seems like I do not specify something correctly in force field but I cannot find my mistake. Shall I specify this connection in specbond.dat file? You do not need specbond.dat. If the CH6 residue is an integral part of the protein backbone, you need to specify the inter-residue bonds using the +/- mechanism with appropriate atom names. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella Sampling - no PMF plateau
Hi Brian, Thanks for this. I checked many windows and I have not observed any unphysical behaviour. I do not have any solvent, its a water-free force field we have developed for the specific system. I do have freely moving LJ beads though. I am thinking i may be the positions restraints dynamics faultbut still not clue. Steven On Tue, Aug 5, 2014 at 11:04 PM, Brian Yoo brian.s.yoo...@nd.edu wrote: Hi Steven, I've run into a similar issue with CG simulations using tabulated potentials. For my system it turns out the continuous increase in PMF was due to the system freezing for some unknown reason. Once I annealed the system (~500 K) and messed around with the temperature coupling, the system unfroze, and I was eventually able to obtain the correct plateau in the PMF curve. Have you checked some of your configurations to see whether your system shows unphysical ordering? (I am assuming you are using an explicit solvent.) Hope this helps, Brian On Tue, Aug 5, 2014 at 5:19 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I run US simulations between 2 nanotubes with attached proteins with distance as a reaction coordinate. This is a coarse-grain simulation, both tubes are placed across pbc so infinite in length. I have tabulated potentials for both bonded and non-bonded interactions. I observed that even at large distances between them in US windows when they do not interact (even across pbc) the PMF is still increasing... no plateau is observed... I tried it in many systems increasing the box size but still the same happening. The perido image is 15 nm away and the cutoff in potentials is 2 nm... Would you please advise? May that correspond to position restraint dynamics of tube atoms of one of them (from which I pulled the other one)? Or maybe tabulated potentials used? Steven -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?
Please compare the file 8.log https://onedrive.live.com/redir?resid=990FCE59E48164A4%212481authkey=%21AI9ThbRY_7ZgAg8ithint=file%2clog and 512.log https://onedrive.live.com/redir?resid=990FCE59E48164A4%212482authkey=%21APLkizOBzXtPHxsithint=file%2clog.Their M E G A - F L O P S A C C O U N T I N part are different as 8.log has no standalone NxN VdW [F] and NxN VdW [VF]. 512.log has the following lines. NxN VdW [F] 17.077648 563.562 0.0 NxN VdW [VF]0.002592 0.111 0.0 Why the difference? And the both have NxN Ewald Elec. + VdW [F] NxN Ewald Elec. + VdW [VF] Does NxN Ewald Elec. + VdW [F] mean NxN Ewald Elec. and NxN VdW [F]? If it is the case, why 512.log has both NxN Ewald Elec. + VdW [F] and NxN VdW [F]? On 8/5/2014 10:11 PM, Mark Abraham wrote: On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si sjyz...@gmail.com wrote: This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. Since the first line and third line both have N*N Vdw [F], does the former include the latter? No, but there is no line with N*N Vdw [F]. Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Velocity Distribution Calculation
Dear all, I am a new user of GROMACS. Now I am using it on water permeability through a nano-channel. The pressure difference is applied by adding acceleration to water molecules in a periodic simulation box. To get the flow rate of water, I need to the number of water molecules through the channel or spatial velocity distribution in different regions. I used to do similar simulations by LAMMPS. LAMMPS provides the function of count (region, group) or the command of fix ave/spatial for counting atom number or velocity distribution. I am wondering how I can do it in GROMACS. Does it have the same commands? I went over the manual and saw commands of g_traj and g_spatial. Are they what I am looking for? Thank you very much for your attention. Best, Jason -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GBSA + infinite cutoff + GPU in GMX5?
Oh ok. Good thing I checked. Thanks! Sandeep On Aug 5, 2014 9:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/5/14, 1:10 PM, Sandeep Somani wrote: Hi Based on the documentation ( http://www.gromacs.org/Documentation/Cut-off_schemes), it seems that, with GMX 5, GBSA implicit solvent simulations with infinite cutoff (rcoulomb = 0, rvdw = 0, pbc = no) cannot be done on GPUs. Is that right? Don't run an implicit simulation on GPU in 5.0; it is not expected to work at all and should be disabled entirely back in version 4.6. See http://redmine.gromacs.org/issues/1570. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
