Re: [gmx-users] A snapshot at a particular time frame
Dear Ravi Use trjconv -dump ... ( time in ps) With Best wishes and regards Rama david. On Mon, Oct 1, 2012 at 11:15 AM, Ravi Kumar Venkatraman ravikumarvenkatra...@gmail.com wrote: Dear All, How to get a snapshot at a particular time frame from the MDS run. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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 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] Binding Energy to Binding affinity (Kd)
Dear Everyone, I have two questions about the conversion of binding energy to binding affinity. I predicted the binding energy of a protein-membrane complex by umbrella sampling (based on Justin's tutorial). After sampling, the binding energy should be the substract of (min-max) PMF. I have repeated the simulation 12 times, and then I have done umbrella samplings also 12 times, then got 12 binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the value vary too much? or is it reasonable since the simulation results can be different? Are those values too huge? When I tried to convert the binding energy to Kd by the formula deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is -100kcal/mol, the kd is calculated as 3.35e-59 μM. The kd is 1.77e-126 μM when binding energy is -200kcal/mol. This is impossible. But what is going wrong? I appreciate any reply. Thanks, Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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] Re: distance restraint
28 sep 2012 kl. 18.53 skrev pauladelgado: Yes i found this document Computer simulations: Orientation of Lysozyme in vacuum under the influence of an electric field where i found about the conditions i mentioned before for vacuum simulations. So what should i do? Find other literature. That document is a master thesis and not peer-reviewed material. I know the supervisor, and also the student to some extent, but even if I'd vouch for the methods used you should base your protocol primarily on peer-reviewed publications. In my former group we published a few papers on protein simulations in vacuo (which were all NVE). See e.g. Patriksson et al, Biochemistry 46:933-945 (2007) Wang et al, Biochemistry 48:1006-1015 (2009) Friemann et al, J. Am. Chem. Soc. 131:16606-+ (2009) Marklund et al, PCCP 11:8069-8078 (2009) Van der Spoel et al, Macromol. Biosci. 11:50-59 (2011) Also have a look at the work of Modesto Orozco. Best, Erik -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001411.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] DNA orientation restrain
Hi, Depending on what you aim to do one option might be to make the DNA a pair of periodic molecules. That would keep them aligned with whatever box vector you chose. But again, that depends on what you aim to study. Erik 1 okt 2012 kl. 07.44 skrev 仝督读: Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX Manual. But the orientation value is set to be observables of NMR experiments, such as this example: ; ai aj type exp. label alpha const. obs. weight 31 32 1 1 3 3 6.083 -6.73 1.0 But how can I set the observable in my case as it's not an NMR experiment? Any suggestion will be appreciate. Thanks very much Dudu Tong 31%2032%201%201%203%203 -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Regarding Torsional energetics
On 10/1/12 12:43 AM, Ravi Kumar Venkatraman wrote: Dear All, To find out gas phase torsional energetics I have restraints dihedral and calculated the energies. But the Dihedral restraints are not working properly, its changes +/- 2-5 degree from the specified value. Is there any other way we can run torsional energetics are I have chenge the modifications in the *.top and *.mdp files. Restraints are simply biasing potentials; they do not fix any parameter at a given value. The dihedral fluctuation is entirely normal. If you want to reduce the fluctuations, increase the value of dihre_fc in the .mdp file. -Justin I made following modifications in my *.top file and *.mdp file to make dihedral restraints. #include dab.itp [ dihedral_restraints ] ; aiaj akal type label phi dphi kfac power 26 2318 6 1 1 0 0 12 ;dihedral restraints dihre = yes dihre_fc= 100 Thank you * With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Binding Energy to Binding affinity (Kd)
On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote: Dear Everyone, I have two questions about the conversion of binding energy to binding affinity. I predicted the binding energy of a protein-membrane complex by umbrella sampling (based on Justin's tutorial). After sampling, the binding energy should be the substract of (min-max) PMF. I have repeated the simulation 12 times, and then I have done umbrella samplings also 12 times, then got 12 binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the value vary too much? or is it reasonable since the simulation results can be different? Are those values too huge? Without an explanation of how long your windows are and what the error estimate for each replicate is, it is impossible to answer this question. When I tried to convert the binding energy to Kd by the formula deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is -100kcal/mol, the kd is calculated as 3.35e-59 μM. The kd is 1.77e-126 μM when binding energy is -200kcal/mol. This is impossible. But what is going wrong? I think you are doing your calculations incorrectly (I obtain your values when using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the mismatch), but even when done properly, the values are still unreasonable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] LINCS WARNING relative constraint deviation
On 10/1/12 7:10 AM, Ali Alizadeh wrote: Dear all users 1- I am trying to simulate a system that contains 1182 methane molecules(5910 atoms) and 1830 water molecules(5490), I keep getting these errors. Something is wrong with the starting configuration, topology, or .mdp settings (see below for comments) such that energy minimization fails almost instantly. http://www.gromacs.org/Documentation/Terminology/Blowing_Up 2- Gromacs does not give me a .xtc file, Why? Perhaps there's some quirk of the code that won't produce an .xtc file with an EM algorithm. EM is normally quick and takes up little disk space, so the benefit to having a compressed trajectory is minimal in most cases. My command lines for grompp and mdrun in terminal window: grompp -f npt.mdp -c wwfull.top.gro -p topol.top -o topol.tpr -n ww.ndx mdrun -s topol.tpr -o wwfull.trr -x wwfull.xtc These are errors and my .mdp file: ... Steepest Descents: Tolerance (Fmax) = 1.0e-04 Number of steps= 1000 Step 50, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000589, max 0.014000 (between atoms 2636 and 2638) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2636 2637 39.40.1090 0.1092 0.1090 Step 51, time 0.0102 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001802, max 0.029832 (between atoms 2026 and 2029) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2331 2334 43.10.1090 0.1093 0.1090 2026 2028 49.60.1090 0.1095 0.1090 5071 5074 41.70.1090 0.1093 0.1090 4806 4808 47.00.1090 0.1095 0.1090 Step 52, time 0.0104 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.003002, max 0.049492 (between atoms 156 and 159) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 471474 51.70.1090 0.1096 0.1090 2331 2334 32.40.1093 0.1078 0.1090 5071 5074 31.30.1093 0.1081 0.1090 156160 55.30.1090 0.1095 0.1090 916919 41.00.1090 0.1093 0.1090 5886 5890 61.10.1090 0.1092 0.1090 Step 53, time 0.0106 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.034606, max 0.843079 (between atoms 5886 and 5890) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 471475 31.50.1049 0.1325 0.1090 471474 92.90.1096 0.1519 0.1090 471473 38.60.1044 0.1402 0.1090 471472 92.70.1048 0.1568 0.1090 2331 2335 48.80.1082 0.1083 0.1090 2331 2334 48.40.1078 0.1070 0.1090 2331 2333 88.80.1110 0.1564 0.1090 2331 2332 88.80.1110 0.1586 0.1090 2026 2030 89.40.1103 0.1177 0.1090 2026 2028 40.00.1091 0.1191 0.1090 2026 2027 38.20.1089 0.1207 0.1090 5071 5075 41.90.1084 0.1048 0.1090 5071 5074 41.60.1081 0.1043 0.1090 5071 5073 88.60.1109 0.1376 0.1090 5071 5072 88.70.1110 0.1392 0.1090 4806 4810 89.30.1104 0.1176 0.1090 4806 4809 32.70.1104 0.0927 0.1090 4806 4808 35.20.1089 0.1140 0.1090 4806 4807 35.00.1088 0.1153 0.1090 156160 92.70.1095 0.1324 0.1090 156159 80.80.1036 0.0523 0.1090 156158 90.00.1036 0.1338 0.1090 156157 90.40.1037 0.1489 0.1090 2276 2280 38.30.1091 0.1114 0.1090 2276 2277 33.00.1089 0.1134 0.1090 2286 2290 37.80.1090 0.1102 0.1090 916920 90.10.1068 0.1704 0.1090 916919 45.90.1093 0.1237 0.1090 916917 65.00.1067 0.1285 0.1090 1296 1300 31.20.1090 0.1094 0.1090 5886 5890 90.90.1092 0.2009 0.1090 5886 5889 47.90.1043 0.1326 0.1090 5886 5888 85.90.1045 0.1282 0.1090 5886 5887 91.40.1046 0.1208 0.1090 Back Off! I just backed up step53b_n0.pdb to ./#step53b_n0.pdb.1# Back Off! I just backed up step53c_n0.pdb to ./#step53c_n0.pdb.1# Wrote pdb files with previous and current coordinates .. .. .. This is my .mdp file: title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.0002 nsteps = 1000 ;
Re: [gmx-users] protein peptide interaction -reg
On 10/1/12 8:52 AM, venkatesh s wrote: Respected Gromacs Users, i am trying to simulate protein peptide want understand interaction my protien 210 Amino acid and my peptide only 5 Amino acid, and molecular types different (between protein peptide ) docked conformation (may i follow Protein ligand tutorial ) No. You should process the peptide ligand with pdb2gmx, not any external topology producing sites. inserting peptide into pdb file or which suitable way i want do in gromacs ? Either will work. The syntax of the coordinate file is all that matters. pdb2gmx can handle multiple proteins in the same file, provided they are separated by TER or have different chain identifiers. pdb2gmx should then produce two topologies (.itp files), one for each protein (the larger protein and the peptide ligand). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Error with grompp
Thanks for your time and help as always. I will see what I can do about that. Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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: [gmx-users] DNA orientation restrain
Dear Dudu Tong Theres a paper on using limited x y z restraints but I have forgotten it. In any case theres a way to generate 1 2 or 3D positional restraints with just the grompp , and you can cut and past. The output posre in the help command will give you a file, and theres a selection for what force you want applied , but If you want only 1 or 2 dimensions you just need a spread sheet editor, and can change 1 or 2 manually after they are generated. Stephan Watkins Original-Nachricht Datum: Mon, 1 Oct 2012 13:44:20 +0800 Von: 仝督读 tongdudu.u...@gmail.com An: gmx-users@gromacs.org Betreff: [gmx-users] DNA orientation restrain Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX Manual. But the orientation value is set to be observables of NMR experiments, such as this example: ; ai aj type exp. label alpha const. obs. weight 31 32 1 1 3 3 6.083 -6.73 1.0 But how can I set the observable in my case as it's not an NMR experiment? Any suggestion will be appreciate. Thanks very much Dudu Tong 31%2032%201%201%203%203 -- 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 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] question about new residue
Hi everybody, I want to do a md run. But I have a problem. I have additional residues which are not in the aminoacid.rtp file. I already read the site about Adding a Residue to a Force Field. But the problem is that I am not allowed to change anything at the topology files on the server I want to run the job. I have to run it on this server because on my computer it would take way to long. So is there another possibility to add the new residues to the topology or offer them to gromacs. Or can I do all the preparing steps until the md run local on my computer where I already changed the topologies so that all the input files which aare produced by grompp and are needed by the md-run are already there. Thank you for your help, Eva -- 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] question about new residue
On 10/1/12 4:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md run. But I have a problem. I have additional residues which are not in the aminoacid.rtp file. I already read the site about Adding a Residue to a Force Field. But the problem is that I am not allowed to change anything at the topology files on the server I want to run the job. I have to run it on this server because on my computer it would take way to long. So is there another possibility to add the new residues to the topology or offer them to gromacs. Or can I do all the preparing steps until the md run local on my computer where I already changed the topologies so that all the input files which aare produced by grompp and are needed by the md-run are already there. You can do all the preparation steps on your own machine. Alternatively, you can always make a copy of the force field directory (and its entire contents) in the working directory and make any changes there. pdb2gmx will detect the directory in the working directory and use its files to generate the topology. Doing so circumvents any permission issues. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] question about new residue
Hi Justin, thank you very much for the helpful and fast answer :) On 10/1/12 4:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md run. But I have a problem. I have additional residues which are not in the aminoacid.rtp file. I already read the site about Adding a Residue to a Force Field. But the problem is that I am not allowed to change anything at the topology files on the server I want to run the job. I have to run it on this server because on my computer it would take way to long. So is there another possibility to add the new residues to the topology or offer them to gromacs. Or can I do all the preparing steps until the md run local on my computer where I already changed the topologies so that all the input files which aare produced by grompp and are needed by the md-run are already there. You can do all the preparation steps on your own machine. Alternatively, you can always make a copy of the force field directory (and its entire contents) in the working directory and make any changes there. pdb2gmx will detect the directory in the working directory and use its files to generate the topology. Doing so circumvents any permission issues. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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
[gmx-users] Force field for ions
Dear all: Does anyone know the optimal force field in GROMACS for treating divalent ions in explicit solvent? Would appreciate any recommendations. Thanks, Lili -- 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] Error with grompp
I am a bit confused..I am getting different errors though similar in goal. The error this time is: Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atomsLet me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an ffoplsaamod.itp, i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files : ffoplsaanb.itp and ffoplsaabon.itp, I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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: [gmx-users] Error with grompp
Hi Elie, Your email is a bit confusing but I will try to give you some idea as per my understanding of your email. If you want to use top and itp files separately, you should put all the info (molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and you should use # include your itp file.itp in your top file. No atom, bond, pair etc in your top file. Just like you include your water type (spc/tip4) you should include the itp. And top of that you should put the right number of molecules in the right order in your top file at the (molecules) section. Hope that might give you some help. Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Elie M Sent: Tuesday, 2 October 2012 1:39 PM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Error with grompp I am a bit confused..I am getting different errors though similar in goal. The error this time is: Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atomsLet me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an ffoplsaamod.itp, i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files : ffoplsaanb.itp and ffoplsaabon.itp, I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie Date: Mon, 1 Oct 2012 08:38:15 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/1/12 12:38 AM, Elie M wrote: Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the error: Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]' I tried to uncomment the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it ffoplsaamod.itp.. Not sure if this has anything to do with the error. It probably does. The first #include statement in your topology is probably: #include ffoplsaa.itp That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have renamed the files, then ffoplsaanb.itp does not occur and cannot be #included prior to ffoplsaabon.itp. The order of inclusion is essential for proper functionality. If you need to make adjustments to the contents of any of these files, make a local copy of the entire force field and make modifications, leaving the files located in $GMXLIB alone. Do not rename them unless you consistently rename all references to these files. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 -- 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] DNA orientation restrain
On Monday 01,October,2012 01:44 PM, 仝督读 wrote: Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX Manual. But the orientation value is set to be observables of NMR experiments, such as this example: ; ai aj type exp. label alpha const. obs. weight 31 32 1 1 3 3 6.083 -6.73 1.0 But how can I set the observable in my case as it's not an NMR experiment? Any suggestion will be appreciate. Thanks very much Dudu, notice the posre.itp? ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 change the fz value to be high enough, like below: 1 1 1000 1000 5 this 5 I just made up here as example, you may try to pick a reasonable one. Dudu Tong 31%2032%201%201%203%203 -- 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_energy menu choices inconsistent?
I have been trying to automate my simulation setup and monitoring. I wrote a script which calls g_energy, and automatically generates plots of potential energy from my EM step, temperature from my NVT equilibration step, and pressure and density from my NPT equilibration step. For each of these three simulations, it appeared that the numbering on the g_energy menu was consistent: Potential = 11, Temperature = 15, Pressure = 16, Density = 22. I wrote my program assuming that these numbers would always describe the parameters listed. Maybe not? Something is still going wrong with my production run, I'm getting a segmentation fault after about 40,000 steps (sigh, I almost thought I had this whole setup understood and debugged). So I used my graphing program to check the temperature, and the results were... odd, bouncing from +300 to -100. The values in my MD.log file disagreed with my graph, they were all within a few degrees of 310K, my target temperature. So I re-ran g_energy directly, bypassing my program, using my production-run ener.edr file as input. The menu showed: Potential = 10, Temperature = 13, Pressure = 15, Density = 21. Seeing this number shift, I understand why my temperature graph for the production looked wrong -- I was actually graphing pressure. Not knowing what menu options to expect will impair my ability to automate the running of g_energy. I can try some tricks to capture that menu each time I run the program, but it will be a chore. I would also like to understand: what is the REASON that these numbers might change between runs? -- View this message in context: http://gromacs.5086.n6.nabble.com/g-energy-menu-choices-inconsistent-tp5001494.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
