[gmx-users] Aquaporin in DOPC
I was able to do the KALP-15 in DPPC. Thanks to the tutorial by Justin Lemkul. Now, I tried to do it with a different protein and lipid. I used aquaporin (protein) and DOPC (lipid) I now have the solvated Aquaporin in DOPC. Now, I'm wondering, should I put ions too? to neutralize the system? If yes, what ion and what charge should I put in my system? I tried to search online I can't see what charge aquaporin has. Thanks! :) -- View this message in context: http://gromacs.5086.x6.nabble.com/Aquaporin-in-DOPC-tp5014072.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_helixorient help
Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] graphics card fail during mdrun
Hello! I was running a simulation using both of the graphics cards on my desktop (I have one Tesla C2075 and one Quadro 2000, which also handles monitor output). I am pretty sure the Quadro 2000 has failed this morning, and I was wondering, what happens to an mdrun in progress when one of the graphics cards fails? -- View this message in context: http://gromacs.5086.x6.nabble.com/graphics-card-fail-during-mdrun-tp5014075.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] can we differentiate it?
No, but genion asks you for a group of solvent molecules to use as the candidates for replacement. You wish to differentiate two different sub-groups, which you can do in advance in your genion -n file, e.g. generated using a geometric criterion in g_select. This kind of Unix-style re-use is why we have a million utilities in GROMACS ;-) Mark On Mon, Jan 27, 2014 at 9:00 AM, Albert mailmd2...@gmail.com wrote: Hi Tsjerk: many thanks for your such helpful advices. If I Turn off PBC in Z-direction, I am just wondering, is it possible to add different salt in each leaflet? For instance: 0.15M NaCl in the up leaflet and 0.15M KCl in the low leaflet? When I use genion command in Gromacs, I don't find any options to do so. thank you very much. Albert On 01/26/2014 10:44 AM, Tsjerk Wassenaar wrote: Hi Albert, Turn off PBC in the z-direction, or introduce a vacuum layer and set the compressibility in the z-direction to zero. Cheers, Tsjerk -- 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] graphics card fail during mdrun
The behavior of most programs in case of a hardware failure is undefined. However, as an MD simulation is quite sensitive to data corruption, the simulation will most often crash immediately after such an event. However, I can also imagine that mdrun ends up hanging, e.g. waiting for data from the GPU. How do you know that the card has failed? In what way did it fail? Were you using both cards? Btw, the Quadro 2000 is a rather slow card, did it really improve performance using it together with the C2075 (in the same run/simulation)? -- Szilárd On Mon, Jan 27, 2014 at 1:38 PM, unitALX alec.zan...@gmail.com wrote: Hello! I was running a simulation using both of the graphics cards on my desktop (I have one Tesla C2075 and one Quadro 2000, which also handles monitor output). I am pretty sure the Quadro 2000 has failed this morning, and I was wondering, what happens to an mdrun in progress when one of the graphics cards fails? -- View this message in context: http://gromacs.5086.x6.nabble.com/graphics-card-fail-during-mdrun-tp5014075.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Aquaporin in DOPC
On 1/27/14, 4:02 AM, jhosamelly wrote: I was able to do the KALP-15 in DPPC. Thanks to the tutorial by Justin Lemkul. Now, I tried to do it with a different protein and lipid. I used aquaporin (protein) and DOPC (lipid) I now have the solvated Aquaporin in DOPC. Now, I'm wondering, should I put ions too? to neutralize the system? If yes, what ion and what charge should I put in my system? Do you know which algorithms require charge neutrality, and are they relevant to you? Which ions make the most sense given what you want to model? NaCl is the most common salt used in most simulations, but you should consider what it is you're trying to model and what concentration might be relevant. I tried to search online I can't see what charge aquaporin has. Because such information doesn't exist, because charge is not an intrinsic property of a protein; it is a function of the environment. You may be able to find a pI value, but the charge the protein bears depends on how you treat it. The total charge of your protein, as determined by the choices you make during pdb2gmx, is stored in the topology. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Rerun error
Does it mean that doing rerun on current md_0_1.trr file is impossible, unless it is transfered to a cluster or a more powerful system? Sincerely, Shima On Sunday, January 26, 2014 11:50 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Thanks for the full description. It seems like your file system cannot handle files over 2gb even for splitting, which is not surprising, because the limitation is based on the use of a 32-bit integer. You should get access to a better file system, where maybe your file can be read. You may wish to consider the advice at http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark On Jan 26, 2014 8:34 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: The error after gmxcheck is: Can not open file: md_0_1.trr The first .trr file was the output of mdrun: grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -n index.ndx -o md_0_1.tpr mpirun -np 32 mdrun_mpi -deffnm md_0_1 -v I just tried to get rerun energy but it failed, then searched in mailing list, found that one of the common problems is the size of .trr file. So tried to split it to 10 files with the size of 2G. This was done in unix. Then tried again to run rerun on the new resized .trr files. Rerun worked just on the first .trr and did not work for the rest of them. Would you please give me suggestions? Thanks. Sincerely, Shima On Fri, 1/24/14, Justin Lemkul jalem...@vt.edu wrote: Subject: Re: [gmx-users] Rerun error To: gmx-us...@gromacs.org, Shima Arasteh shima_arasteh2...@yahoo.com Date: Friday, January 24, 2014, 12:40 PM On 1/24/14, 1:56 PM, Shima Arasteh wrote: On Friday, January 24, 2014 9:09 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: I tried trjconv -f md_0_1.trr -s md_0_1.tpr -split 1000 -o md_0_1_new.trr My system does not recognize the md_0_1.trr file. oh... :-( Would you please help me? Providing a single command does not help much. What does does not recognize mean? What is the *exact* error? How was md_0_1.trr generated in the first place and how does it relate to the other files shown in the commands below? -Justin Sincerely, Shima On Friday, January 24, 2014 8:23 PM, Mark Abraham mark.j.abra...@gmail.com wrote: You're using unix split? That could work for .trr under the right conditions, but apparently it is not. trjconv has a million different ways to split trajectories, so try them. Also chekc that your file system can handle files bigger than 2GB at all. Mark On Fri, Jan 24, 2014 at 5:40 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Making a new folder didn't solve my problem unfortunately. The commands I ran are these: 1.Split files larger than 2G split -b 2097152000 md_0_1.trr -d The output files are: x00 x01 x02 . . . x10 Then: 2.grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -o md_rerun_0.tpr -n index.ndx 3.mdrun -rerun x00.trr -s md_rerun_0.tpr -e md_rerun_0.edr -o md_rerun_0.trr -v Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: gmx-us...@gromacs.org gmx-us...@gromacs.org Sent: Friday, January 24, 2014 7:19 PM Subject: Re: [gmx-users] Rerun error So there's nothing in it. Maybe mdrun over-write it according to Christian's theory, but since we don't know what your commands were, we're guessing... The extra 30 seconds of copy-pasting your commands from your terminal would have led to an answer by now! Mark On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Last frame -1 time 0.000 # Atoms -1 Last frame -1 time 0.000 Item #frames Timestep (ps) Step 0 Time 0 Lambda 0 Coords 0 Velocities 0 Forces 0 Box 0 Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org; Shima Arasteh shima_arasteh2...@yahoo.com Sent: Friday, January 24, 2014 6:43 PM Subject: Re: [gmx-users] Rerun error What does gmxcheck say about this files? Mark On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi, I had a large .trr file, tried to do rerun on it. First I used split command and made 10 new .trr files with 2G in size. Then ran rerun on the first 2G.trr, but this does not work for the rest of trr files and I get the error: The number of atoms in trajectory (-1) doesn't match the input file. Would you please
Re: [gmx-users] Rerun error
Yes. You need to read the positions to do a rerun. To do that, you need to be able to read the file. Mark On Mon, Jan 27, 2014 at 7:25 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Does it mean that doing rerun on current md_0_1.trr file is impossible, unless it is transfered to a cluster or a more powerful system? Sincerely, Shima On Sunday, January 26, 2014 11:50 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Thanks for the full description. It seems like your file system cannot handle files over 2gb even for splitting, which is not surprising, because the limitation is based on the use of a 32-bit integer. You should get access to a better file system, where maybe your file can be read. You may wish to consider the advice at http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark On Jan 26, 2014 8:34 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: The error after gmxcheck is: Can not open file: md_0_1.trr The first .trr file was the output of mdrun: grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -n index.ndx -o md_0_1.tpr mpirun -np 32 mdrun_mpi -deffnm md_0_1 -v I just tried to get rerun energy but it failed, then searched in mailing list, found that one of the common problems is the size of .trr file. So tried to split it to 10 files with the size of 2G. This was done in unix. Then tried again to run rerun on the new resized .trr files. Rerun worked just on the first .trr and did not work for the rest of them. Would you please give me suggestions? Thanks. Sincerely, Shima On Fri, 1/24/14, Justin Lemkul jalem...@vt.edu wrote: Subject: Re: [gmx-users] Rerun error To: gmx-us...@gromacs.org, Shima Arasteh shima_arasteh2...@yahoo.com Date: Friday, January 24, 2014, 12:40 PM On 1/24/14, 1:56 PM, Shima Arasteh wrote: On Friday, January 24, 2014 9:09 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: I tried trjconv -f md_0_1.trr -s md_0_1.tpr -split 1000 -o md_0_1_new.trr My system does not recognize the md_0_1.trr file. oh... :-( Would you please help me? Providing a single command does not help much. What does does not recognize mean? What is the *exact* error? How was md_0_1.trr generated in the first place and how does it relate to the other files shown in the commands below? -Justin Sincerely, Shima On Friday, January 24, 2014 8:23 PM, Mark Abraham mark.j.abra...@gmail.com wrote: You're using unix split? That could work for .trr under the right conditions, but apparently it is not. trjconv has a million different ways to split trajectories, so try them. Also chekc that your file system can handle files bigger than 2GB at all. Mark On Fri, Jan 24, 2014 at 5:40 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Making a new folder didn't solve my problem unfortunately. The commands I ran are these: 1.Split files larger than 2G split -b 2097152000 md_0_1.trr -d The output files are: x00 x01 x02 . . . x10 Then: 2.grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -o md_rerun_0.tpr -n index.ndx 3.mdrun -rerun x00.trr -s md_rerun_0.tpr -e md_rerun_0.edr -o md_rerun_0.trr -v Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: gmx-us...@gromacs.org gmx-us...@gromacs.org Sent: Friday, January 24, 2014 7:19 PM Subject: Re: [gmx-users] Rerun error So there's nothing in it. Maybe mdrun over-write it according to Christian's theory, but since we don't know what your commands were, we're guessing... The extra 30 seconds of copy-pasting your commands from your terminal would have led to an answer by now! Mark On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Last frame -1 time0.000 # Atoms -1 Last frame -1 time0.000 Item#frames Timestep (ps) Step 0 Time 0 Lambda 0 Coords 0 Velocities 0 Forces 0 Box 0 Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org; Shima Arasteh shima_arasteh2...@yahoo.com Sent: Friday, January 24, 2014 6:43 PM Subject: Re: [gmx-users] Rerun error What does gmxcheck say about this files? Mark On Fri, Jan 24, 2014 at 3:49 PM, Shima
Re: [gmx-users] Pull code vs. manual pull for umbrella sampling
Hello, As I had explained earlier, I have done MD at varied protein bi-layer distances. I now want to create a probability distribution histogram along the reaction coordinate I generated by varying the distances. I know I can concatenate various .trr files I have from various MD runs with different initial starting configurations. Is there a way to obtain the probability distribution histogram. Kindly help. Thanks, sxn Shivangi Nangia, Ph. D Postdoctoral Research Associate Department of Molecular and Cell Biology University of Connecticut On Fri, Jan 24, 2014 at 3:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/24/14, 3:50 PM, shivangi nangia wrote: Dear Justin, Okay, so I have multiple configurations of protein and bi-layer system (30 initial configurations) at varied distances (in steps of 0.05 nm). The protein has been moved away with respect to its COM. So I have manually pulled the protein away from the bi-layer instead of using the pull code. I have run MD simulations for each of these configurations. I need to use g_wham to calculate the PMF and for that I need the pullx.xvg files. It won't be possible. What you did wasn't umbrella sampling, it was just MD. If there is no restraint potential applied during the simulations in each of the sampling windows, there's nothing to de-bias to reconstruct a free energy profile. You can generate the configurations in any manner you like (manually or by using the pull code), but the umbrella sampling itself requires the use of the pull code. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] Pull code vs. manual pull for umbrella sampling
On 1/27/14, 3:49 PM, shivangi nangia wrote: Hello, As I had explained earlier, I have done MD at varied protein bi-layer distances. I now want to create a probability distribution histogram along the reaction coordinate I generated by varying the distances. I know I can concatenate various .trr files I have from various MD runs with different initial starting configurations. There is no need to concatenate trajectories. In fact, that will probably make your life harder having one massive trajectory. I suspect you'll want the distributions from each individual trajectory, anyway. Is there a way to obtain the probability distribution histogram. That's what g_analyze -distr does. Feed it the output of g_dist. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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] multiple GPU on multiple nodes
Hi guys I am using a CrayXK7 machine with one GPU (Tesla K20) per node (one AMD Opteron 16-core Interlagos x86_64). Currently I am trying to run the gromacs gpu version using only two nodesbut it is not working. When I tried using one node and one gpu it works aprun -n 1 mdrun_mpi -deffnm filename when I try two nodes and two GPUs, it does not work (these are the ways that I had tried) aprun -n 2 mdrun_mpi -deffnm filename aprun -n 2 mdrun_mpi -gpu_id 00 -deffnm filename aprun -n 2 mdrun_mpi -gpu_if 0011 -deffnm filename aprun -n 32 mdrun_mpi -deffnm filename aprun -n 32 mdrun_mpi -gpu_id 00 -deffnm filename aprun -n 32 mdrun_mpi -gpu_if 0011 -deffnm filename Sometimes I got errors like: Program mdrun_mpi, VERSION 4.6.2 Source code file: /N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #0: insane GPU #0: insane For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Program mdrun_mpi, VERSION 4.6.2 Source code file: /N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/statutil.c, line: 976 Invalid command line argument: 0 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors 1 GPU detected on host nid00900: #0: NVIDIA Tesla K20, compute cap.: 3.5, ECC: yes, stat: compatible --- Program mdrun_mpi, VERSION 4.6.2 Source code file: /N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent GPU #1: inexistent For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors 1 GPU detected on host nid00900: #0: NVIDIA Tesla K20, compute cap.: 3.5, ECC: yes, stat: compatible Compiled acceleration: None (Gromacs could use AVX_128_FMA on this machine, which is better) --- Program mdrun_mpi, VERSION 4.6.2 Source code file: /N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/gmx_detect_hardware.c, line: 356 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 2 PP MPI processes per node, but only 1 GPU were detected. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If you have any idea how make it work, please let me know John Michael -- 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 in grompp for protein-ligand tutorial
I am new to Gromacs, then follow the tutorial protein-ligand, decided to adapt the procedure for my protein (acetylcholinesterase) and my binder. The procedure is this (protein-ligand complex): http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/comp lex/index.html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl ex/index.html Well, I switched to facilitate the name of my protein and my binder by the names used in the tutorial. The problem occurs when I do the command: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr The following error occurs: Fatal error: Molecule type 'Protein_chain_A' contains no atoms I do not know how I can fix so please help me. -- 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] At what point is the random seed generated?
On 2014-01-28 08:37, Trayder Thomas wrote: Hi, When using 'gen-seed = -1' at what point is the random seed assigned? e.g. Does it use the process ID of grompp and embed the seed number in the tpr file, or does it use the process ID of mdrun? I ask because I have 50 identical simulations started from the same tpr file :( Thanks, -Trayder I guess you found out. Sorry about that. It is done in grompp and same tpr should give reproducible results. So you want to generate 50 different tpr files. -- 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.
