Re: [gmx-users] Annealing of shell polarizable water model
Dear Justin, Dear all you guessed right. I am now using a v-rescale thermostate and it works fine and it also runs in parallel. Here below the changed part in my grompp with the v-rescale thermostate. Thanks a lot Ivan ### ;OPTIONS FOR ANNELING annealing = single annealing_npoints = 2 annealing_time = 0 1000 annealing_temp = 0 160 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ;Nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 160.00 ## On 03/22/2011 01:09 PM, Justin A. Lemkul wrote: Ivan Gladich wrote: Dear David Dear all I did the serial run with the same topology and grompp: even if the simulation time is still short (due by the serial run), the temperature profiles are the same (see attached file). As further check, I removed the annealing and the temperature rises to 160 K after ~0.5ps without problem. So I do not think that it is a problem of the shell polarizability with the running in parallel. Could be a problem of the shell polarizability with annealing? You could test that relatively easily with a simple box of water. The result would be useful. Other than that, maybe the thermostat itself is causing the problem? I always do annealing with a weak coupling method, not Nose-Hoover. I've had stability problems with unequilibrated systems with N-H. In principle, it shouldn't matter, but setting tcoupl to Berendsen and/or V-rescale would be another very useful diagnostic. -Justin Thanks again Ivan On 03/22/2011 10:45 AM, Ivan Gladich wrote: Yes, I am running in parallel... Now I will try to run in serial to see if the problem persist Thanks Ivan On 03/22/2011 10:00 AM, David van der Spoel wrote: On 2011-03-22 10.37, Ivan Gladich wrote: Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of water has 4 sites plus a shell and I am using a small time step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns. To do that I used a linear annealing from 0 to 160 K. Are you running in parallel? Unfortunately polarizable MD is broken on more than 1 core. There is a redmine issue for this, and it will be fixed soon. The simulation runs without problem but I cannot reach the desire temperature. In other words, if I look my md.log file I can see the ref_t that linear increase from 0 to 160 K in 1 ns but the system temperature seems to do not follow the thermostate temperature. If I plot the temperature obtained from g_energy, the temperature of the system remains constant at ~36 K. I attach also my temperature profile up to 600ps. Due to the small time step the simulation takes a bit of time but it is clear that the temperature remain constant I have tried to find in the mail list some similar problem without success... Here below I report my grompp. Maybe I missed something. Thank in advance for any suggestions. Ivan #3 ; VARIOUS PREPROCESSING OPTIONS title = Ice SWM4-NDP cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md dt = 0.0001 nsteps = 1400 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 1000 ; Output frequency and precision for xtc file nstxtcout = 1 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.1 ;domain-decomposition = ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.1 ; Method for doing Van der Waals vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.1 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 optimize_fft = no ;OPTIONS FOR ANNELING annealing = single annealing_npoints = 2 annealing_time = 0 1000 annealing_temp = 0 160 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = Nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 160.00
[gmx-users] Re: Parameterization of a molecule containing a radical, (oxygen) (Justin A. Lemkul)
There is a AMBER FF for this kind of nitroxide spin labels. See PCCP 12 (2010) 11697. Hope it helps, Gerrit Simone Cirri wrote: Hi all, I have a question regarding a new parameterization: actually, I'm wondering whether or not it is possible to do it. The molecule is tempol; you cand find its PubChem entry here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs As you can see, the problem of this molecule is its O radical; this, and the N belonging to the cycle too. My lab would really benefit from the parameterization (for the AMBER force field) of tempol, since we commonly use it in our NMR experiments. We don't know how to treat the oxygen radical and the N bound to it, though. If this parameterization is impossible to do we will give up, but we would like to be sure about it. Thanks in advance for any answer you could provide. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs This would not be a trivial molecule to parameterize. You could start by using antechamber (available free as part of AmberTools), since it allows you to tune multiplicity (-m flag). Otherwise, the existing force fields may not provide a suitable atom type for the O radical or its effects on the rest of the molecule. I still don't know if parameterization would be possible for a standard MM force field (though it very well might), but this might get you started. -Justin -- Simone Cirri -- 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] how to differentiate crystal water and explicit waters in gromacs ???
On 23/03/2011 4:42 PM, Praveen Kumar Madala wrote: Hi, I am new to GROMACS and I am trying to perform a MD run in PBC condition with water as solvent. I want to keep the crystal water molecules different from explicit waters, I believe this helps me in analysis of crystal waters. You can set up an index group to label them, and then use a visualization or other analysis program to see what they do. This doesn't require doing anything prior to the simulation. See manual and webpage for resources describing use and construction of groups. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx
Just an update, I decided to create a new residue for an isolated GMP. Well, not really, because I used pdb2gmx to output a topology of a dimer, and then modified it carefully to extract the topology of a phosphorylated GTP. thank you ! On Tue, Mar 22, 2011 at 2:52 PM, maria goranovic mariagorano...@gmail.comwrote: the gro file was the input. I am attaching a pdb as well CRYST1100.0100.0100.0 90.00 90.00 90.00 P 1 1 ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00 P ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00 O ATOM 3 OP2 G A 4 5.367 -1.998 1.624 1.00 0.00 O ATOM 4 O5' G A 4 4.010 -0.213 0.513 1.00 0.00 O ATOM 5 C5' G A 4 3.816 1.098 0.014 1.00 0.00 C ATOM 6 C4' G A 4 2.324 1.432 -0.121 1.00 0.00 C ATOM 7 O4' G A 4 1.623 0.448 -0.862 1.00 0.00 O ATOM 8 C3' G A 4 1.584 1.482 1.211 1.00 0.00 C ATOM 9 O3' G A 4 1.869 2.669 1.934 1.00 0.00 O ATOM 10 C2' G A 4 0.136 1.413 0.721 1.00 0.00 C ATOM 11 O2' G A 4 -0.363 2.696 0.397 1.00 0.00 O ATOM 12 C1' G A 4 0.241 0.597 -0.574 1.00 0.00 C ATOM 13 N9 G A 4 -0.450 -0.705 -0.438 1.00 0.00 N ATOM 14 C8 G A 4 0.075 -1.954 -0.237 1.00 0.00 C ATOM 15 N7 G A 4 -0.808 -2.911 -0.197 1.00 0.00 N ATOM 16 C5 G A 4 -2.017 -2.251 -0.377 1.00 0.00 C ATOM 17 C6 G A 4 -3.346 -2.767 -0.450 1.00 0.00 C ATOM 18 O6 G A 4 -3.705 -3.941 -0.398 1.00 0.00 O ATOM 19 N1 G A 4 -4.299 -1.762 -0.593 1.00 0.00 N ATOM 20 C2 G A 4 -4.002 -0.413 -0.682 1.00 0.00 C ATOM 21 N2 G A 4 -5.023 0.438 -0.804 1.00 0.00 N ATOM 22 N3 G A 4 -2.751 0.071 -0.652 1.00 0.00 N ATOM 23 C4 G A 4 -1.809 -0.897 -0.499 1.00 0.00 C ATOM 24 H5' G A 4 4.293 1.204 -0.960 1.00 0.00 H ATOM 25 H5'' G A 4 4.269 1.819 0.696 1.00 0.00 H ATOM 26 H4' G A 4 2.217 2.395 -0.623 1.00 0.00 H ATOM 27 H3' G A 4 1.819 0.589 1.792 1.00 0.00 H ATOM 28 H2' G A 4 -0.503 0.940 1.465 1.00 0.00 H ATOM 29 HO2' G A 4 -1.301 2.614 0.210 1.00 0.00 H ATOM 30 H1' G A 4 -0.225 1.145 -1.393 1.00 0.00 H ATOM 31 H8 G A 4 1.129 -2.132 -0.139 1.00 0.00 H ATOM 32 H1 G A 4 -5.265 -2.065 -0.635 1.00 0.00 H ATOM 33 H21 G A 4 -5.974 0.099 -0.815 1.00 0.00 H ATOM 34 H22 G A 4 -4.841 1.428 -0.876 1.00 0.00 H END On Tue, Mar 22, 2011 at 2:43 PM, Daniel Adriano Silva M dadri...@gmail.com wrote: Hi, Is this your input? (a GRO file?). Can you paste the PDB corresponding to the RNA nucleotide that you are interested on? I think the file may be small enough to paste it here so someone can try to reproduce what is happening to you. Daniel 2011/3/22 maria goranovic mariagorano...@gmail.com Sorry for the incomplete reply. version 4.5.3, command: pdb2gmx -f guan.pdb -ignh I tried using -ter, but that did not help. input coordinate file, pulled out from an RNA molecule. Gromacs Runs On Most of All Computer Systems 34 1GP1 5.549 4.916 5.071 1G OP12 5.642 5.026 5.105 1G OP23 5.537 4.800 5.162 1G O5'4 5.401 4.979 5.051 1G C5'5 5.382 5.110 5.001 1G C4'6 5.232 5.143 4.988 1G O4'7 5.162 5.045 4.914 1G C3'8 5.158 5.148 5.121 1G O3'9 5.187 5.267 5.193 1G C2' 10 5.014 5.141 5.072 1G O2' 11 4.964 5.270 5.040 1G C1' 12 5.024 5.060 4.943 1G N9 13 4.955 4.930 4.956 1G C8 14 5.008 4.805 4.976 1G N7 15 4.919 4.709 4.980 1G C5 16 4.798 4.775 4.962 1G C6 17 4.665 4.723 4.955 1G O6 18 4.630 4.606 4.960 1G N1 19 4.570 4.824 4.941 1G C2 20 4.600 4.959 4.932 1G N2 21 4.498 5.044 4.920 1G N3 22 4.725 5.007 4.935 1G C4 23 4.819 4.910 4.950 1G H5' 24 5.429 5.120 4.904 1G H5'' 25 5.427 5.182 5.070 1G H4' 26 5.222 5.240 4.938 1G H3' 27 5.182 5.059 5.179 1G H2' 28 4.950 5.094 5.146 1G HO2' 29 4.870 5.261 5.021 1G H1' 30 4.978 5.115 4.861 1G H8 31 5.113 4.787
[gmx-users] angular velocity autocorrelation
Dear Users, I need to calculate the angular velocity correlation function. From the gromacs discussion forum, I understand that one should be able to use g_rotacf to calculate the angular velocity correlation function ( http://oldwww.gromacs.org/pipermail/gmx-users/2004-September/012278.html). However, when I look into the g_rotacf function, if I am not mistaken, the rotational correlation function gives us the autocorrelation of the normal vector to the two vectors defined in the input. It does not provide the angular velocity correlation function. Could someone give me pointers as to how one can calculate the angular velocity correlation function from g_rotacf? I need this information to analyze the density of states distribution. Any help is greatly appreciated. Thank you, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)
Hello users, Although there was already much discussion had been done on the procedure to construct DCCM map from covar.dat(i.e. output from g_covar) but still I am not clear with the step wise procedure to calculate the correlation matrix from covarience matrix(covar.dat). 1) It is stated in the previous posts that to calculate correlation matrix we have to divide each i,j-th element of the covariance matrix (covar.dat) by the sqrt of the ii-th and jj-th diagonal element, but how to get diagonal of a 865107X3 matrix??? 2) As given in the manual the order of elements in covar.dat is is: x1x1,x1y1, x1z1, x1x2, ... But I am not clear which are i,j-th ,ii-th and jj-th elements in covar.dat. My covarience matrix have 865107 rows and 3 columns and the total atoms are 537(sqrt( 865107 X 3) / 3=537 atoms) Can anyone suggest how to transform the covar.dat into correlation matrix. I am expecting the stepwise procedure to construct the correlation matrix and not the theory behind it as it already stated in the previous posts. -- --- *Regards,* Bipin Singh -- 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] Various web issues
Hi Justin, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: 1. manual.gromacs.org no longer has any useful content. The site comes up with syrah.cbr.su.se and nothing else. Are there changes going on with this site? I moved the manual to the new server and now it's accessible again. Cheers, Rossen -- 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] %hbond number problem
Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n,and the output info is nothing? So, could you tell me the correct usage? Very thanks! There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section: 1 2603 1 2619 1 2634 1 2635 1 2 1299 1942 1943 1917 1937 1939113 1937 1939114 - xiaodu My simulation system contains protein, dna and water. I used your script already for obtaining %exist hydrogen bonds between protein and dna-- 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] LINCS warning on galactose molecule
Dear gmx-users, I'm experimenting a LINCS warning on my system, an enzyme with ATP, galactose and Mg. We started from the crystallographic structure, made some accommodation on the topology of the sugar in order to check for partial charges (according to Justin Lemkul's suggestions on PRODRG server), then performed a minimization, NVT and NPT PR-MD and the production MD. After about 5 ns of simulation the MD stopped with the LINCS error: Step 2562553, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000102, max 0.001903 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 45.3 0.1000 0.1000 0.1000 Step 2562554, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000104, max 0.001558 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 36.5 0.1000 0.1000 0.1000 Step 2562565, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000318, max 0.007712 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 31.5 0.1005 0.1008 0.1000 Step 2562566, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000374, max 0.009231 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.2 0.1008 0.1009 0.1000 Step 2562567, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000310, max 0.007658 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.6 0.1009 0.1008 0.1000 Step 2563563, time 5127.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.70, max 0.001640 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 57.0 0.0998 0.1002 0.1000 --- Program mdrun, VERSION 4.0.3 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- We checked the system to find the problem. The atoms 7641 and 7640 correspond to atom O1 and H12 of the galactose. With VMD we visualized the trajectory, but we did not see anything anomalous on this bond. Length and angles are quite normal. This OH group is near the phosphate of ATP but the distances seem to be compatible with an (expected) H-bond. I don't think the problem could be an incorrect stabilization because it seems to me that in that case the problem would have appear during the first step of MD, not after 5 ns. In any case, stabilization went correctly, with no errors or warnings. I checked on the gmx-users list and found some messages of Xavier Periole experimenting some LINCS problems with gmx 4.0.4, that seems to resemble my situation. I followed the thread, but I did not see anything that could be of help for me. Some hypotheses were about the gmx version (mine is 4.0.3), communications between CPUs, virtual sites. Looking at the trajectory, I don't think it's a problem of periodic images too close. The thread stops with Xavier saying he would like to test the effects of using -rdd and -rcon on LINCS warning, but I did not find the rest of the history. Does anybody (and especially Xavier, if possible!) have some hints about my problem? Or could it be a problem of galactose topology? Thank you very much and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man -- 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] %hbond number problem
Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n,and the output info is nothing? So, could you tell me the correct usage? Very thanks! There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section: 1 2603 1 2619 1 2634 1 2635 1 2 1299 1942 1943 1917 1937 1939113 1937 1939114 - xiaodu -- 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 on galactose molecule
On 23/03/2011 9:45 PM, Anna Marabotti wrote: Dear gmx-users, I'm experimenting a LINCS warning on my system, an enzyme with ATP, galactose and Mg. We started from the crystallographic structure, made some accommodation on the topology of the sugar in order to check for partial charges (according to Justin Lemkul's suggestions on PRODRG server), then performed a minimization, NVT and NPT PR-MD and the production MD. After about 5 ns of simulation the MD stopped with the LINCS error: Step 2562553, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000102, max 0.001903 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 45.3 0.1000 0.1000 0.1000 Step 2562554, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000104, max 0.001558 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 36.5 0.1000 0.1000 0.1000 Step 2562565, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000318, max 0.007712 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 31.5 0.1005 0.1008 0.1000 Step 2562566, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000374, max 0.009231 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.2 0.1008 0.1009 0.1000 Step 2562567, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000310, max 0.007658 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.6 0.1009 0.1008 0.1000 Step 2563563, time 5127.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.70, max 0.001640 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 57.0 0.0998 0.1002 0.1000 --- Program mdrun, VERSION 4.0.3 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- We checked the system to find the problem. The atoms 7641 and 7640 correspond to atom O1 and H12 of the galactose. With VMD we visualized the trajectory, but we did not see anything anomalous on this bond. Length and angles are quite normal. This OH group is near the phosphate of ATP but the distances seem to be compatible with an (expected) H-bond. I don't think the problem could be an incorrect stabilization because it seems to me that in that case the problem would have appear during the first step of MD, not after 5 ns. In any case, stabilization went correctly, with no errors or warnings. I checked on the gmx-users list and found some messages of Xavier Periole experimenting some LINCS problems with gmx 4.0.4, that seems to resemble my situation. I followed the thread, but I did not see anything that could be of help for me. Some hypotheses were about the gmx version (mine is 4.0.3), communications between CPUs, virtual sites. Looking at the trajectory, I don't think it's a problem of periodic images too close. The thread stops with Xavier saying he would like to test the effects of using -rdd and -rcon on LINCS warning, but I did not find the rest of the history. Does anybody (and especially Xavier, if possible!) have some hints about my problem? Or could it be a problem of galactose topology? Usually the problem has nothing to do with LINCS or -rdd or -con - they're just symptoms of machinery that breaks first. I'd start by assuming my topologies were not well-formed somehow, and divide and conquer to locate the problem. Can you simulate galactose in vacuo? In a small water box? Same for ATP. Same for enzyme. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit of surface tension, KJ/mol?
On 23/03/2011 3:39 PM, Elisabeth wrote: Thanks Mark for the hints. I am using a pre equilibrated box for both runs. Can you again explain how Can I interpret this from fluctuations from two runs? Below is the resutls from two versions: Thanks! IIRC the contents of the .edr file didn't change across these versions, but the reporting of computed quantities did, so I'd make my life simpler and use only the 4.5.3 g_energy. Both simulations have a much higher value for the root-mean-squared deviation from the average (i.e. standard deviation) than for the average. So that means your data set looks something like 1 20 6543 200 23444 23434 15 500 3444. Look at the .xvg file that is produced. You need a heck of a lot of such data to have confidence that your sample average reflects the true average. If you haven't got that pile of data, then you haven't observed the average with any confidence. This is normal for quantities computed from fluctuations in atomic positions. They're macroscopic quantities, and have to be observed over a lot of microscopic configurations. Be sure to check visually that your system is doing what you hope it is doing. Mark 4.0.7 Statistics over 733801 steps [ 0. thru 1467.6001 ps ], 1 data sets All averages are exact over 733801 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 203.7783623.993623.98 -0.00203751 -2.99026 Statistics over 483401 steps [ 500. thru 1466.8000 ps ], 1 data sets All averages are exact over 483401 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 203.1293612.583612.28 0.168686163.086 - 4.5.3 Statistics over 732501 steps [ 1. through 1466. ps ], 1 data sets All statistics are over 73251 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 2374.4957021081.3 -3251.38 (bar nm) Statistics over 384501 steps [ 1000. through 1769. ps ], 1 data sets All statistics are over 38451 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 2610.25 100021109.94638.38 (bar nm) Statistics over 483001 steps [ 500. through 1466. ps ], 1 data sets All statistics are over 48301 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 1645.0739020288.3 -174.289 (bar nm) On 22 March 2011 23:56, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/03/11, *Elisabeth * katesed...@gmail.com mailto:katesed...@gmail.com wrote: On 22 March 2011 22:46, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: On 22 March 2011 22:31, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the same in these versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted into bar nm? Can anyone help please. Is this from g_energy output? In past versions, everything was printed as kJ/mol, even quantities that obviously weren't, like temperature, pressure, etc. Yes, so why are the results so different. I am using exactly the same mdp file.! Any pressure-related quantity is going to be subject to enormous fluctuations. This has been discussed within the last few days. Without seeing the .mdp file and a description of the system, it's hard for anyone to comment on what the results might mean. Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is extended in Z to create liq/air interface. That is 3X3X6 . What could be reason for such a big difference in results from two version? Thanks alot! Look at the size of the fluctuations printed by
Re: [gmx-users] unit of surface tension, KJ/mol?
Mark Abraham wrote: On 23/03/2011 3:39 PM, Elisabeth wrote: Thanks Mark for the hints. I am using a pre equilibrated box for both runs. Can you again explain how Can I interpret this from fluctuations from two runs? Below is the resutls from two versions: Thanks! IIRC the contents of the .edr file didn't change across these versions, but the reporting of computed quantities did, so I'd make my life simpler and use only the 4.5.3 g_energy. Actually, 4.5.3 may have the bug: http://redmine.gromacs.org/issues/696 The quantities in the .edr file are correct, but the output from g_energy is nonsense. It was fixed for 4.5.4. -Justin Both simulations have a much higher value for the root-mean-squared deviation from the average (i.e. standard deviation) than for the average. So that means your data set looks something like 1 20 6543 200 23444 23434 15 500 3444. Look at the .xvg file that is produced. You need a heck of a lot of such data to have confidence that your sample average reflects the true average. If you haven't got that pile of data, then you haven't observed the average with any confidence. This is normal for quantities computed from fluctuations in atomic positions. They're macroscopic quantities, and have to be observed over a lot of microscopic configurations. Be sure to check visually that your system is doing what you hope it is doing. Mark 4.0.7 Statistics over 733801 steps [ 0. thru 1467.6001 ps ], 1 data sets All averages are exact over 733801 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 203.7783623.993623.98 -0.00203751 -2.99026 Statistics over 483401 steps [ 500. thru 1466.8000 ps ], 1 data sets All averages are exact over 483401 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 203.1293612.583612.28 0.168686163.086 - 4.5.3 Statistics over 732501 steps [ 1. through 1466. ps ], 1 data sets All statistics are over 73251 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 2374.4957021081.3 -3251.38 (bar nm) Statistics over 384501 steps [ 1000. through 1769. ps ], 1 data sets All statistics are over 38451 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 2610.25 100021109.94638.38 (bar nm) Statistics over 483001 steps [ 500. through 1466. ps ], 1 data sets All statistics are over 48301 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 1645.0739020288.3 -174.289 (bar nm) On 22 March 2011 23:56, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/03/11, *Elisabeth * katesed...@gmail.com mailto:katesed...@gmail.com wrote: On 22 March 2011 22:46, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: On 22 March 2011 22:31, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the same in these versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted into bar nm? Can anyone help please. Is this from g_energy output? In past versions, everything was printed as kJ/mol, even quantities that obviously weren't, like temperature, pressure, etc. Yes, so why are the results so different. I am using exactly the same mdp file.! Any pressure-related quantity is going to be subject to enormous fluctuations. This has been discussed within the last few days. Without seeing the .mdp file and a description of the system, it's hard for anyone to comment on what the results might mean. Thanks. I am working on a pure alkane system, in a box of 3X3X3
Re: [gmx-users] %hbond number problem
gromacs564 wrote: Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n,and the output info is nothing? So, could you tell me the correct usage? Very thanks! There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section: 1 2603 1 2619 1 2634 1 2635 1 2 1299 1942 1943 1917 1937 1939113 1937 1939114 - xiaodu My simulation system contains protein, dna and water. I used your script already for obtaining %exist hydrogen bonds between protein and dna Then doesn't this imply that you know how to run it? Neither of the above commands is correct. The first uses $0, which is a perl construct for the name of the program. The second contains a newline (\n) character, although the format of this command is what you should use (without the newline, which is printed by the program to the screen as help information). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] unit of surface tension, KJ/mol?
Thanks for your help. :) On 23 March 2011 07:47, Justin A. Lemkul jalem...@vt.edu wrote: Mark Abraham wrote: On 23/03/2011 3:39 PM, Elisabeth wrote: Thanks Mark for the hints. I am using a pre equilibrated box for both runs. Can you again explain how Can I interpret this from fluctuations from two runs? Below is the resutls from two versions: Thanks! IIRC the contents of the .edr file didn't change across these versions, but the reporting of computed quantities did, so I'd make my life simpler and use only the 4.5.3 g_energy. Actually, 4.5.3 may have the bug: http://redmine.gromacs.org/issues/696 The quantities in the .edr file are correct, but the output from g_energy is nonsense. It was fixed for 4.5.4. -Justin Both simulations have a much higher value for the root-mean-squared deviation from the average (i.e. standard deviation) than for the average. So that means your data set looks something like 1 20 6543 200 23444 23434 15 500 3444. Look at the .xvg file that is produced. You need a heck of a lot of such data to have confidence that your sample average reflects the true average. If you haven't got that pile of data, then you haven't observed the average with any confidence. This is normal for quantities computed from fluctuations in atomic positions. They're macroscopic quantities, and have to be observed over a lot of microscopic configurations. Be sure to check visually that your system is doing what you hope it is doing. Mark 4.0.7 Statistics over 733801 steps [ 0. thru 1467.6001 ps ], 1 data sets All averages are exact over 733801 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 203.7783623.993623.98 -0.00203751 -2.99026 Statistics over 483401 steps [ 500. thru 1466.8000 ps ], 1 data sets All averages are exact over 483401 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 203.1293612.583612.28 0.168686 163.086 - 4.5.3 Statistics over 732501 steps [ 1. through 1466. ps ], 1 data sets All statistics are over 73251 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 2374.4957021081.3 -3251.38 (bar nm) Statistics over 384501 steps [ 1000. through 1769. ps ], 1 data sets All statistics are over 38451 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 2610.25 100021109.94638.38 (bar nm) Statistics over 483001 steps [ 500. through 1466. ps ], 1 data sets All statistics are over 48301 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 1645.0739020288.3 -174.289 (bar nm) On 22 March 2011 23:56, Mark Abraham mark.abra...@anu.edu.au mailto: mark.abra...@anu.edu.au wrote: On 23/03/11, *Elisabeth * katesed...@gmail.com mailto:katesed...@gmail.com wrote: On 22 March 2011 22:46, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: On 22 March 2011 22:31, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Elisabeth wrote: Hello, I did two simulations on the same system using versions 4.0.7 and 4.5.3. It seems like the unit of surface tension is not the same in these versions because I am getting ~250 KJ/mol an in 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted into bar nm? Can anyone help please. Is this from g_energy output? In past versions, everything was printed as kJ/mol, even quantities that obviously weren't, like temperature, pressure, etc. Yes, so why are the results so different. I am using exactly the same mdp file.! Any pressure-related quantity is going to be subject to enormous fluctuations. This has been discussed within the last few days. Without seeing the .mdp file and a description of the system, it's hard for anyone to
[gmx-users] no output dgdl file
Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- 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] no output dgdl file
Moeed wrote: Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). How long has the simulation been running? Output is buffered, and I find that dhdl.xvg is not updated often. free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none Note that turning off all interactions simultaneously (especially when using soft-core) can be very unstable. You should (de)couple vdW and Coulombic interactions separately. -Justin couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] compressing a box of water droplets into a homogeneous solution of liquid water
Hi Chris, I experienced the same kind of thing. In the process of building a box of liquid (organic solvent), at some point I wanted to get rid of a layer of vacuum around my system. So for shrinking the box I used similar settings as you and found also that the collapse was going slower than I'd have expected. One solution to accelerate this (if your goal is to shrink the box) is to increase the pressure (to say 100 atm). But it's important to stop the simulation in time (i.e. once the layer of vacuum has disapeared) otherwise the system shrinks too much and density is off. So to come back to your system which has a very big layer of vacuum around, and according to my experience, the volume is probably decreasing but too slowly to see anything signigicant (compared to the initial value) in 200 ps . Ciao, Patrick Le 21/03/2011 16:53, chris.ne...@utoronto.ca a écrit : Dear users: I recently came across a system that was composed of tip4p water vapor droplets separated by vacuum. This system is what you might get if you did a NVT simulation of water with a box that was 10 times too large for the number of water molecules. I was surprised to see that this system did not collapse to any significant extent during 200 ps of NPT equilibration at 1 atm using the Berendsen thermostat with tau_p=1.0 and the sd integrator and a colombic cut-off. (We also tried a number of other integrator/pressure coupling combinations with the same results). I had assumed that such collapse would occur quite rapidly. This does not seem to be the case (no noticeable contraction within 200 ps). Has anybody else done anything like this? Can anybody comment on their expectations/experience of collapse from the gas state to the liquid state under standard NPT conditions? Thank you, Chris. -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] compressing a box of water droplets into a homogeneous solution of liquid water
Hi Chris, recently one of my students made a mistake during the model system assembling, setting the initial volume to a value three times larger than expected by the density. after 1 microsecond (coarse grained MD, of course) there were droplets and vacuum between them, and the volume did not shrink until we applied a 100 bar pressure to the external bath (using Berendsen's weak coupling with the default setting for the Martini FF). on the other hand, recently I was trying to model the methanol gas phase using the OPLS-AA FF and I found out it was a very tricky kind of model, as different systems with different volumes but the same (gas phase) density yielded quite different results, ranging from only one droplet (smaller system) to a distribution with more than 99% of monomers (larger system). from my standpoint, what happened to the smaller systems should be regarded as an artefact due to finite size of the system, thus only the results for the larger system got published, as I was not interested in the discussion of the artefact itself. best regards, André On Wed, Mar 23, 2011 at 3:48 PM, Patrick Fuchs patrick.fu...@univ-paris-diderot.fr wrote: Hi Chris, I experienced the same kind of thing. In the process of building a box of liquid (organic solvent), at some point I wanted to get rid of a layer of vacuum around my system. So for shrinking the box I used similar settings as you and found also that the collapse was going slower than I'd have expected. One solution to accelerate this (if your goal is to shrink the box) is to increase the pressure (to say 100 atm). But it's important to stop the simulation in time (i.e. once the layer of vacuum has disapeared) otherwise the system shrinks too much and density is off. So to come back to your system which has a very big layer of vacuum around, and according to my experience, the volume is probably decreasing but too slowly to see anything signigicant (compared to the initial value) in 200 ps . Ciao, Patrick Le 21/03/2011 16:53, chris.ne...@utoronto.ca a écrit : Dear users: I recently came across a system that was composed of tip4p water vapor droplets separated by vacuum. This system is what you might get if you did a NVT simulation of water with a box that was 10 times too large for the number of water molecules. I was surprised to see that this system did not collapse to any significant extent during 200 ps of NPT equilibration at 1 atm using the Berendsen thermostat with tau_p=1.0 and the sd integrator and a colombic cut-off. (We also tried a number of other integrator/pressure coupling combinations with the same results). I had assumed that such collapse would occur quite rapidly. This does not seem to be the case (no noticeable contraction within 200 ps). Has anybody else done anything like this? Can anybody comment on their expectations/experience of collapse from the gas state to the liquid state under standard NPT conditions? Thank you, Chris. -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing list gmx-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] no output dgdl file
Hi Justin, I was looking all the time for a file with dgdl extension throughout the directory. IIRC in previous versions -dgdl would generate such extension. I found now .xvg file which has dhdl data. (if I am right dgdl is the very dhdl in 4.5.3!) I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). How long has the simulation been running? Output is buffered, and I find that dhdl.xvg is not updated often. free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none Note that turning off all interactions simultaneously (especially when using soft-core) can be very unstable. You should (de)couple vdW and Coulombic interactions separately. Yes I read your comment about decoupling separately earlier on but I was not sure if this could depend upon the system so I was thinking of comparing results from two trials: trial 1: couple-lambda0 = vdw-q couple-lambda1 = none trail 2 A: couple-lambda0 = vdw-q couple-lambda1 = vdw trail 2 B couple-lambda0 = vdw couple-lambda1 = none So: 1- Does this decoupling issue depend on the system or it is a must for all FE studies? 2- I actually went through many of FE posts and never found how separete decoupling can be done. from trail 2 A and B I get dgdl files but how to get total vdw-q to none from these two? Please shed some light on the details of procedure.. 3- With free_energy turned off my runs take only a few hours but as I shift to free_energy = yes, runs take nearly one day foe each lambda.. Is this normal for s system having 2500 atoms? Thanks Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] compressing a box of water droplets into a homogeneous solution of liquid water
Thanks Patrick and Andre! We repeated this with a few box sizes just to get a quick handle on it. The equilibrium volume is about 64 nm^3. If we start with a volume of 1000 nm^3 then the overall box does not collapse at all within 200 ps of NPT Langevin dynamics at 1 atm.If we start with a volume of 200 nm^3, then it does collapse to approximately 64 nm^3 within 200 ps of such simulation. My best guess is that the rapid collapse is driven by nonbonded interactions and thus the rapid collapse does not occur when the system is so large with such low density that water forms isolated vapour droplets that do not interact with each other by LJ interactions. Sure, it is expected to collapse eventually from the 1 atm pressure coupling, and we have also observed that high pressure works, but at 1 atm it might take a very long time to reach equilibrium. I agree with Andre that none of this matters to regular simulations as there is no good reason to go through this type of state when one wants to simulate dense liquids. I just found it curious that Berendsen pressure coupling at 1 atm was not sufficient to quickly equilibrate the volume in a system where the vacuum regions are large in comparison to the LJ cutoffs. Chris. -- original message -- Hi Chris, I experienced the same kind of thing. In the process of building a box of liquid (organic solvent), at some point I wanted to get rid of a layer of vacuum around my system. So for shrinking the box I used similar settings as you and found also that the collapse was going slower than I'd have expected. One solution to accelerate this (if your goal is to shrink the box) is to increase the pressure (to say 100 atm). But it's important to stop the simulation in time (i.e. once the layer of vacuum has disapeared) otherwise the system shrinks too much and density is off. So to come back to your system which has a very big layer of vacuum around, and according to my experience, the volume is probably decreasing but too slowly to see anything signigicant (compared to the initial value) in 200 ps . Ciao, Patrick Le 21/03/2011 16:53, chris.ne...@utoronto.ca a écrit : [Hide Quoted Text] Dear users: I recently came across a system that was composed of tip4p water vapor droplets separated by vacuum. This system is what you might get if you did a NVT simulation of water with a box that was 10 times too large for the number of water molecules. I was surprised to see that this system did not collapse to any significant extent during 200 ps of NPT equilibration at 1 atm using the Berendsen thermostat with tau_p=1.0 and the sd integrator and a colombic cut-off. (We also tried a number of other integrator/pressure coupling combinations with the same results). I had assumed that such collapse would occur quite rapidly. This does not seem to be the case (no noticeable contraction within 200 ps). Has anybody else done anything like this? Can anybody comment on their expectations/experience of collapse from the gas state to the liquid state under standard NPT conditions? Thank you, Chris. -- 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] account for PBC
ahmet yıldırım wrote: Dear Justin, You said You didn't properly account for PBC. Watch the trajectory - you should see distinct jumps across the box. for attached figure. What should I do? Exactly as I said. Watch the trajectory to see if my guess is right. If the molecule is dancing back and forth across PBC, it explains what you're seeing with the RMSD. Fix the PBC issues with trjconv, if that is indeed the case. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] no output dgdl file
Moeed wrote: Hi Justin, I was looking all the time for a file with dgdl extension throughout the directory. IIRC in previous versions -dgdl would generate such extension. I found now .xvg file which has dhdl data. (if I am right dgdl is the very dhdl in 4.5.3!) The extension has always been .xvg, but the root filename has changed. It is now perhaps a bit more accurate (delta Hamiltonian). I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). How long has the simulation been running? Output is buffered, and I find that dhdl.xvg is not updated often. free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none Note that turning off all interactions simultaneously (especially when using soft-core) can be very unstable. You should (de)couple vdW and Coulombic interactions separately. Yes I read your comment about decoupling separately earlier on but I was not sure if this could depend upon the system so I was thinking of comparing results from two trials: trial 1: couple-lambda0 = vdw-q couple-lambda1 = none trail 2 A: couple-lambda0 = vdw-q couple-lambda1 = vdw trail 2 B couple-lambda0 = vdw couple-lambda1 = none So: 1- Does this decoupling issue depend on the system or it is a must for all FE studies? No, it pertains to the very stability of all calculations. Whenever I've decoupled charges and LJ simultaneously, either the simulations crash or the resulting energies are not reliable. There are numerous book chapters and papers dedicated to these topics. 2- I actually went through many of FE posts and never found how separete decoupling can be done. from trail 2 A and B I get dgdl files but how to get total vdw-q to none from these two? Please shed some light on the details of procedure.. Add them. DeltaG is a state function. 3- With free_energy turned off my runs take only a few hours but as I shift to free_energy = yes, runs take nearly one day foe each lambda.. Is this normal for s system having 2500 atoms? Yes. The free energy code slows down runs quite a bit. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] no output dgdl file
Hi, Your foreign_lambda value is only one, please put all your lambda values separated by space and you will get the dhdl file. And make sure that you use -deffnm when you run your mdrun to get all the out put files by default. Cheers, From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Moeed Sent: Thursday, 24 March 2011 4:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] no output dgdl file Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- 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] no output dgdl file
Emanuel Birru wrote: Hi, Your foreign_lambda value is only one, please put all your lambda values separated by space and you will get the dhdl file. And make sure that This is not required. You can specify as many or as few foreign_lambda values as you like. you use –deffnm when you run your mdrun to get all the out put files by default. The -deffnm flag controls the names of the files, not which ones are written. -Justin Cheers, *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed *Sent:* Thursday, 24 March 2011 4:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] no output dgdl file Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] no output dgdl file
Emanuel Birru wrote: Hi Justin, Sure what you wrote is correct, what I am trying to tell to him is that if he has more than one foreign lambda it is better to put all of them as it is not logical to use only one foreign lambda to calculate FE (0 - 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about You can do a series of simulations at many values of lambda, each specifying their own foreign_lambda. It seems to me that this method would be more reliable, but I have not tested simply attempting a single simulation with all values of foreign_lambda. Using delta_lambda is (from all that I have read) not reliable, as there are known issues with slow growth methods. file names but it also generate all the necessary files including the xvg's without the need of using -dhdl. Whether or not one specifies -dhdl or -deffnm is independent of whether or not dhdl.xvg (or whatever name) is written. It is controlled purely by the presence of free_energy = yes in the input file. I would appreciate if you come up with a new solution for him. As reported by the OP, this issue had been effectively solved already: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html -Justin Cheers -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi, Your foreign_lambda value is only one, please put all your lambda values separated by space and you will get the dhdl file. And make sure that This is not required. You can specify as many or as few foreign_lambda values as you like. you use -deffnm when you run your mdrun to get all the out put files by default. The -deffnm flag controls the names of the files, not which ones are written. -Justin Cheers, *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed *Sent:* Thursday, 24 March 2011 4:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] no output dgdl file Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] No cut-off
Hello everybody, I want to use the no cut-off option in gromacs for the electrostatic interactions. In manual it says for this I need to define: pbc=no; nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. My questions are: 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do you always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option? 2. How should I choose the table-extension parameter now? Before, with pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of the longest diagonal of the box (approximately). I am also using a tabulated potential. Thank you, -Swarnendu -- 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] no output dgdl file
Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because free_energy = yes is present. The problem with the 4.5.3 is not the problem of generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess the main advantage of using 4.5.3 to calculated FE using foreign_lambda was to avoid running series of independent simulations. May be it is solved on the newer version 4.5.4., didn't try it yet. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:54 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, Sure what you wrote is correct, what I am trying to tell to him is that if he has more than one foreign lambda it is better to put all of them as it is not logical to use only one foreign lambda to calculate FE (0 - 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about You can do a series of simulations at many values of lambda, each specifying their own foreign_lambda. It seems to me that this method would be more reliable, but I have not tested simply attempting a single simulation with all values of foreign_lambda. Using delta_lambda is (from all that I have read) not reliable, as there are known issues with slow growth methods. file names but it also generate all the necessary files including the xvg's without the need of using -dhdl. Whether or not one specifies -dhdl or -deffnm is independent of whether or not dhdl.xvg (or whatever name) is written. It is controlled purely by the presence of free_energy = yes in the input file. I would appreciate if you come up with a new solution for him. As reported by the OP, this issue had been effectively solved already: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html -Justin Cheers -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi, Your foreign_lambda value is only one, please put all your lambda values separated by space and you will get the dhdl file. And make sure that This is not required. You can specify as many or as few foreign_lambda values as you like. you use -deffnm when you run your mdrun to get all the out put files by default. The -deffnm flag controls the names of the files, not which ones are written. -Justin Cheers, *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed *Sent:* Thursday, 24 March 2011 4:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] no output dgdl file Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 foreign_lambda = 0.1 dhdl_derivatives = yes couple-moltype = Polymer couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 Best -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] no output dgdl file
Emanuel Birru wrote: Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda This is certainly a viable method, but it is thermodynamic integration, not BAR. The purpose of lambda/foreign_lambda is to use the BAR method. and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because free_energy = yes is present. The problem with the 4.5.3 is not the problem of It has always been my experience (in versions 3.3.3 and 4.5.3) that if the free energy code is activated, this file is written. I never specify the file names independently. generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess If you suspect a bug, you should report it. If you don't use foreign_lambda, you can't use the BAR method. You're doing TI, not BAR. They are fundamentally different, and the analysis for TI is done independently of any Gromacs tool. the main advantage of using 4.5.3 to calculated FE using foreign_lambda was to avoid running series of independent simulations. May be it is solved on the newer version 4.5.4., didn't try it yet. Version 4.5.3 has worked just fine for all free energy calculations I have done. Perhaps BAR can be done with a single simulation and multiple foreign_lambda, but that was not my understanding of the proper procedure (based on some posts by developers a few months ago). Multiple simulations, each at native lambda, are conducted with values of foreign_lambda above and below the native value at some lambda spacing (except for end points). Invoking g_bar gives the total DeltaG over all lambda intervals according to the BAR algorithm. -Justin Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:54 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, Sure what you wrote is correct, what I am trying to tell to him is that if he has more than one foreign lambda it is better to put all of them as it is not logical to use only one foreign lambda to calculate FE (0 - 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about You can do a series of simulations at many values of lambda, each specifying their own foreign_lambda. It seems to me that this method would be more reliable, but I have not tested simply attempting a single simulation with all values of foreign_lambda. Using delta_lambda is (from all that I have read) not reliable, as there are known issues with slow growth methods. file names but it also generate all the necessary files including the xvg's without the need of using -dhdl. Whether or not one specifies -dhdl or -deffnm is independent of whether or not dhdl.xvg (or whatever name) is written. It is controlled purely by the presence of free_energy = yes in the input file. I would appreciate if you come up with a new solution for him. As reported by the OP, this issue had been effectively solved already: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html -Justin Cheers -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi, Your foreign_lambda value is only one, please put all your lambda values separated by space and you will get the dhdl file. And make sure that This is not required. You can specify as many or as few foreign_lambda values as you like. you use -deffnm when you run your mdrun to get all the out put files by default. The -deffnm flag controls the names of the files, not which ones are written. -Justin Cheers, *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed *Sent:* Thursday, 24 March 2011 4:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] no output dgdl file Hello, I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3). free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3
RE: [gmx-users] no output dgdl file
Yeah, I am using IT and do analyse the result using another method not bar. But I used g_bar when I was using the foreign_lambda and simulate all in a single file. I have already sent my suspect few weeks back. I am a bit confused on the g_bar part, when it says -f expects multiple dhdl files. Do we need to run still multiple independent simulations using different foreign_lambda values? I do not see why we should run independent simulations, if we use for couple-lambda0 and couple-lambda1 vdw-q and none respectively. For IT I am using 4.5.3 and it is working good so far. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 1:36 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda This is certainly a viable method, but it is thermodynamic integration, not BAR. The purpose of lambda/foreign_lambda is to use the BAR method. and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because free_energy = yes is present. The problem with the 4.5.3 is not the problem of It has always been my experience (in versions 3.3.3 and 4.5.3) that if the free energy code is activated, this file is written. I never specify the file names independently. generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess If you suspect a bug, you should report it. If you don't use foreign_lambda, you can't use the BAR method. You're doing TI, not BAR. They are fundamentally different, and the analysis for TI is done independently of any Gromacs tool. the main advantage of using 4.5.3 to calculated FE using foreign_lambda was to avoid running series of independent simulations. May be it is solved on the newer version 4.5.4., didn't try it yet. Version 4.5.3 has worked just fine for all free energy calculations I have done. Perhaps BAR can be done with a single simulation and multiple foreign_lambda, but that was not my understanding of the proper procedure (based on some posts by developers a few months ago). Multiple simulations, each at native lambda, are conducted with values of foreign_lambda above and below the native value at some lambda spacing (except for end points). Invoking g_bar gives the total DeltaG over all lambda intervals according to the BAR algorithm. -Justin Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:54 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, Sure what you wrote is correct, what I am trying to tell to him is that if he has more than one foreign lambda it is better to put all of them as it is not logical to use only one foreign lambda to calculate FE (0 - 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about You can do a series of simulations at many values of lambda, each specifying their own foreign_lambda. It seems to me that this method would be more reliable, but I have not tested simply attempting a single simulation with all values of foreign_lambda. Using delta_lambda is (from all that I have read) not reliable, as there are known issues with slow growth methods. file names but it also generate all the necessary files including the xvg's without the need of using -dhdl. Whether or not one specifies -dhdl or -deffnm is independent of whether or not dhdl.xvg (or whatever name) is written. It is controlled purely by the presence of free_energy = yes in the input file. I would appreciate if you come up with a new solution for him. As reported by the OP, this issue had been effectively solved already: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html -Justin Cheers -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi, Your foreign_lambda value is only one, please put all your lambda values separated by space and you will get the dhdl file. And make sure that This is not required. You
Re: [gmx-users] No cut-off
Hi Swarnendu, grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should stick to it. Cheers, Itamar On 24/03/11 1:13 PM, Swarnendu Tripathi wrote: Hello everybody, I want to use the no cut-off option in gromacs for the electrostatic interactions. In manual it says for this I need to define: pbc=no; nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. My questions are: 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do you always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option? 2. How should I choose the table-extension parameter now? Before, with pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of the longest diagonal of the box (approximately). I am also using a tabulated potential. Thank you, -Swarnendu -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] no output dgdl file
Emanuel Birru wrote: Yeah, I am using IT and do analyse the result using another method not bar. But I used g_bar when I was using the foreign_lambda and simulate all in a single file. I have already sent my suspect few weeks back. Is there an active redmine issue? I cannot find any post from you in the list archive from the last few months. What is the issue? I am a bit confused on the g_bar part, when it says -f expects multiple dhdl files. Do we need to run still multiple independent simulations using different foreign_lambda values? I do not see why we should run independent simulations, if we use for couple-lambda0 and couple-lambda1 vdw-q and none respectively. As I mentioned to the OP of this thread, simultaneous (de)coupling of vdW and Coulombic interactions is not stable. The output energies are not trustworthy, in my experience due to physically unreasonable configurations and the potential for numerical singularities. The multiple files that g_bar expects are not simply from two separate processes, however. It expects dhdl.xvg files from multiple values of native lambda that have corresponding foreign_lambda values in it, i.e.: Interval 1: init_lambda = 0 foreign_lambda = 0.05 Interval 2: init_lambda = 0.05 foreign_lambda = 0 0.1 Interval 3: init_lambda = 0.1 foreign_lambda = 0.05 0.15 etc. -Justin For IT I am using 4.5.3 and it is working good so far. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 1:36 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda This is certainly a viable method, but it is thermodynamic integration, not BAR. The purpose of lambda/foreign_lambda is to use the BAR method. and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because free_energy = yes is present. The problem with the 4.5.3 is not the problem of It has always been my experience (in versions 3.3.3 and 4.5.3) that if the free energy code is activated, this file is written. I never specify the file names independently. generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess If you suspect a bug, you should report it. If you don't use foreign_lambda, you can't use the BAR method. You're doing TI, not BAR. They are fundamentally different, and the analysis for TI is done independently of any Gromacs tool. the main advantage of using 4.5.3 to calculated FE using foreign_lambda was to avoid running series of independent simulations. May be it is solved on the newer version 4.5.4., didn't try it yet. Version 4.5.3 has worked just fine for all free energy calculations I have done. Perhaps BAR can be done with a single simulation and multiple foreign_lambda, but that was not my understanding of the proper procedure (based on some posts by developers a few months ago). Multiple simulations, each at native lambda, are conducted with values of foreign_lambda above and below the native value at some lambda spacing (except for end points). Invoking g_bar gives the total DeltaG over all lambda intervals according to the BAR algorithm. -Justin Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 12:54 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, Sure what you wrote is correct, what I am trying to tell to him is that if he has more than one foreign lambda it is better to put all of them as it is not logical to use only one foreign lambda to calculate FE (0 - 0.1) and he doesn't have delta lambda too. -Deffnm is sure all about You can do a series of simulations at many values of lambda, each specifying their own foreign_lambda. It seems to me that this method would be more reliable, but I have not tested simply attempting a single simulation with all values of foreign_lambda. Using delta_lambda is (from all that I have read) not reliable, as there are known issues with slow growth methods. file names but it also generate all the necessary files including the xvg's without the need of using -dhdl. Whether or not one specifies -dhdl or -deffnm is independent of whether or not dhdl.xvg (or
RE: [gmx-users] no output dgdl file
I have tried the free energy calculation using 4.5.3, but when I run g_bar it still gives me the following and do not generate the output files. prod.xvg: 0.0 - 5000.0; lambda = 0.000 foreign lambdas: 0.000 (125001 pts) 0.000 (125001 pts) 0.010 (125001 pts) 0.030 (125001 pts) 0.050 (125001 pts) 0.100 (125001 pts) 0.200 (125001 pts) 0.300 (125001 pts) 0.400 (125001 pts) 0.500 (125001 pts) 0.600 (125001 pts) 0.650 (125001 pts) 0.700 (125001 pts) 0.750 (125001 pts) 0.800 (125001 pts) 0.850 (125001 pts) 0.900 (125001 pts) 0.950 (125001 pts) 1.000 (125001 pts) No results to calculate. I put my mdp file for production run and the output file prod.xvg on the following links for your consideration. http://hydra.pharm.monash.edu.au/md_project/production.txt (mdp file) http://hydra.pharm.monash.edu.au/md_project/prod.txt (xvg file) Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 2:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Yeah, I am using IT and do analyse the result using another method not bar. But I used g_bar when I was using the foreign_lambda and simulate all in a single file. I have already sent my suspect few weeks back. Is there an active redmine issue? I cannot find any post from you in the list archive from the last few months. What is the issue? I am a bit confused on the g_bar part, when it says -f expects multiple dhdl files. Do we need to run still multiple independent simulations using different foreign_lambda values? I do not see why we should run independent simulations, if we use for couple-lambda0 and couple-lambda1 vdw-q and none respectively. As I mentioned to the OP of this thread, simultaneous (de)coupling of vdW and Coulombic interactions is not stable. The output energies are not trustworthy, in my experience due to physically unreasonable configurations and the potential for numerical singularities. The multiple files that g_bar expects are not simply from two separate processes, however. It expects dhdl.xvg files from multiple values of native lambda that have corresponding foreign_lambda values in it, i.e.: Interval 1: init_lambda = 0 foreign_lambda = 0.05 Interval 2: init_lambda = 0.05 foreign_lambda = 0 0.1 Interval 3: init_lambda = 0.1 foreign_lambda = 0.05 0.15 etc. -Justin For IT I am using 4.5.3 and it is working good so far. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 1:36 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda This is certainly a viable method, but it is thermodynamic integration, not BAR. The purpose of lambda/foreign_lambda is to use the BAR method. and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because free_energy = yes is present. The problem with the 4.5.3 is not the problem of It has always been my experience (in versions 3.3.3 and 4.5.3) that if the free energy code is activated, this file is written. I never specify the file names independently. generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess If you suspect a bug, you should report it. If you don't use foreign_lambda, you can't use the BAR method. You're doing TI, not BAR. They are fundamentally different, and the analysis for TI is done independently of any Gromacs tool. the main advantage of using 4.5.3 to calculated FE using foreign_lambda was to avoid running series of independent simulations. May be it is solved on the newer version 4.5.4., didn't try it yet. Version 4.5.3 has worked just fine for all free energy calculations I have done. Perhaps BAR can be done with a single simulation and multiple foreign_lambda, but that was not my understanding of the proper procedure (based on some posts by developers a few months ago). Multiple simulations, each at native lambda, are conducted with values of foreign_lambda above and below the native value at some lambda spacing (except for end points). Invoking g_bar gives the total DeltaG over all lambda intervals according to the BAR algorithm. -Justin Cheers,
Re: [gmx-users] no output dgdl file
Emanuel Birru wrote: I have tried the free energy calculation using 4.5.3, but when I run g_bar it still gives me the following and do not generate the output files. prod.xvg: 0.0 - 5000.0; lambda = 0.000 foreign lambdas: 0.000 (125001 pts) 0.000 (125001 pts) 0.010 (125001 pts) 0.030 (125001 pts) 0.050 (125001 pts) 0.100 (125001 pts) 0.200 (125001 pts) 0.300 (125001 pts) 0.400 (125001 pts) 0.500 (125001 pts) 0.600 (125001 pts) 0.650 (125001 pts) 0.700 (125001 pts) 0.750 (125001 pts) 0.800 (125001 pts) 0.850 (125001 pts) 0.900 (125001 pts) 0.950 (125001 pts) 1.000 (125001 pts) No results to calculate. I put my mdp file for production run and the output file prod.xvg on the following links for your consideration. http://hydra.pharm.monash.edu.au/md_project/production.txt (mdp file) http://hydra.pharm.monash.edu.au/md_project/prod.txt (xvg file) From the above g_bar output and the .xvg file, it seems that lambda=0 is considered both native and foreign, which probably causes the algorithm to fail. Note, too, that the results in the first column of the .xvg file (which would correspond to some weird difference between lambda=0 and lambda=0, which should not exist!) also seem to be nonsensically high. This is what I mean when I say weird results from simultaneous (de)coupling of charges and LJ terms. The systems are not completely stable, yielding weird energies. The result could also be some bizarre result of lambda=0 being considered native and foreign. Based on the .mdp file, I don't know how this could have happened, but all signs point to some sort of problem with the input. -Justin Cheers, Emanuel -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 2:02 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Yeah, I am using IT and do analyse the result using another method not bar. But I used g_bar when I was using the foreign_lambda and simulate all in a single file. I have already sent my suspect few weeks back. Is there an active redmine issue? I cannot find any post from you in the list archive from the last few months. What is the issue? I am a bit confused on the g_bar part, when it says -f expects multiple dhdl files. Do we need to run still multiple independent simulations using different foreign_lambda values? I do not see why we should run independent simulations, if we use for couple-lambda0 and couple-lambda1 vdw-q and none respectively. As I mentioned to the OP of this thread, simultaneous (de)coupling of vdW and Coulombic interactions is not stable. The output energies are not trustworthy, in my experience due to physically unreasonable configurations and the potential for numerical singularities. The multiple files that g_bar expects are not simply from two separate processes, however. It expects dhdl.xvg files from multiple values of native lambda that have corresponding foreign_lambda values in it, i.e.: Interval 1: init_lambda = 0 foreign_lambda = 0.05 Interval 2: init_lambda = 0.05 foreign_lambda = 0 0.1 Interval 3: init_lambda = 0.1 foreign_lambda = 0.05 0.15 etc. -Justin For IT I am using 4.5.3 and it is working good so far. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 1:36 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: Hi Justin, It good that the issue is solved. As per my experience if you want to do a series of simulations it is not necessary to use foreign_lambda, for each simulation we can give different lambda values starting from 0 to 1( from fully interactive to non-interactive) no need of foreign_lamda This is certainly a viable method, but it is thermodynamic integration, not BAR. The purpose of lambda/foreign_lambda is to use the BAR method. and certainly no need of generating dhdl.xvg to calculate FE. I think -dhdl is an optional it will not be generated just because free_energy = yes is present. The problem with the 4.5.3 is not the problem of It has always been my experience (in versions 3.3.3 and 4.5.3) that if the free energy code is activated, this file is written. I never specify the file names independently. generating dhdl data by using single simulation with all foreign_lambda values. The problem is with g_bar, when I tried to analyse the dhdl.xvg output (with all the necessary data in it) using g_bar, it doesn't function properly. The error is related with the source code. I guess If you suspect a bug, you should report it. If you don't use foreign_lambda, you can't use the BAR method. You're doing TI, not BAR. They are fundamentally different, and the analysis for TI is done independently of any Gromacs tool. the main advantage of
RE: [gmx-users] no output dgdl file
Thanks Justin, I will revise my mdp file again and will give it a try once more. Can you give me an idea on the following too. I want to perform free energy calculation by changing the gd (dihedral parameters) to fourier dihedral parameters for small molecules (solutes). But I am getting the following error when I do grompp, Program grompp, VERSION 4.5.3 Source code file: topsort.c, line: 112 Fatal error: Function type Fourier Dih. not implemented in ip_pert For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is there any simple solution for this or is it a source code error? Here http://hydra.pharm.monash.edu.au/md_project/penteg.top it is my topology file. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 2:35 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: -- 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] no output dgdl file
Emanuel Birru wrote: Thanks Justin, I will revise my mdp file again and will give it a try once more. Can you give me an idea on the following too. I want to perform free energy calculation by changing the gd (dihedral parameters) to fourier dihedral parameters for small molecules (solutes). But I am getting the following error when I do grompp, Program grompp, VERSION 4.5.3 Source code file: topsort.c, line: 112 Fatal error: Function type Fourier Dih. not implemented in ip_pert For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is there any simple solution for this or is it a source code error? The manual states that Fourier dihedrals can have any of their coefficients perturbed, but this does not appear to actually be implemented. Please file a redmine issue so that it can be fixed. -Justin Here http://hydra.pharm.monash.edu.au/md_project/penteg.top it is my topology file. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 24 March 2011 2:35 PM To: Gromacs Users' List Subject: Re: [gmx-users] no output dgdl file Emanuel Birru wrote: -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] No cut-off
On 24/03/2011 1:34 PM, Itamar Kass wrote: Hi Swarnendu, grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should stick to it. Cheers, Itamar On 24/03/11 1:13 PM, Swarnendu Tripathi wrote: Hello everybody, I want to use the no cut-off option in gromacs for the electrostatic interactions. In manual it says for this I need to define: pbc=no; nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. My questions are: 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do you always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option? 2. How should I choose the table-extension parameter now? Before, with pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of the longest diagonal of the box (approximately). I am also using a tabulated potential. Since there is effectively no box once pbc=no, your tables need only be as long as the longest possible interaction, plus some margin for when the structure rearranges. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] No cut-off
Hi all, Thank you for the reply. The answer I got for the second question about table-extension, I understand and agree with that. Regarding my first question I asked, I did not get any error with grompp even when I tried rlist=rvdw=2.0 and rcoulomb=0. For this I used the no cut-off conditions which I have mentioned below in my previous e-mail. I am using Gromacs-4.0.7. Any further suggestions or comments will be very helpful. Thank you, -Swarnendu On Thu, Mar 24, 2011 at 12:17 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/03/2011 1:34 PM, Itamar Kass wrote: Hi Swarnendu, grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should stick to it. Cheers, Itamar On 24/03/11 1:13 PM, Swarnendu Tripathi wrote: Hello everybody, I want to use the no cut-off option in gromacs for the electrostatic interactions. In manual it says for this I need to define: pbc=no; nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. My questions are: 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do you always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option? 2. How should I choose the table-extension parameter now? Before, with pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of the longest diagonal of the box (approximately). I am also using a tabulated potential. Since there is effectively no box once pbc=no, your tables need only be as long as the longest possible interaction, plus some margin for when the structure rearranges. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] No cut-off
On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote: Hi all, Thank you for the reply. The answer I got for the second question about table-extension, I understand and agree with that. Regarding my first question I asked, I did not get any error with grompp even when I tried rlist=rvdw=2.0 and rcoulomb=0. For this I used the no cut-off conditions which I have mentioned below in my previous e-mail. I am using Gromacs-4.0.7. Any further suggestions or comments will be very helpful. VDW interactions normally become insignificant much faster than Coulomb interactions, so treating all Coulomb interactions and only some VDW interactions is logical. However, performing the search for neighbours takes time, and given that you are computing the distances already for their Coulomb interaction, it is probably cheaper just to compute all the VDW interactions, i.e. rlist=rvdw=0. This might be different if you had a lot of atoms that had zero partial charge. Mark On Thu, Mar 24, 2011 at 12:17 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 24/03/2011 1:34 PM, Itamar Kass wrote: Hi Swarnendu, grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should stick to it. Cheers, Itamar On 24/03/11 1:13 PM, Swarnendu Tripathi wrote: Hello everybody, I want to use the no cut-off option in gromacs for the electrostatic interactions. In manual it says for this I need to define: pbc=no; nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. My questions are: 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do you always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option? 2. How should I choose the table-extension parameter now? Before, with pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of the longest diagonal of the box (approximately). I am also using a tabulated potential. Since there is effectively no box once pbc=no, your tables need only be as long as the longest possible interaction, plus some margin for when the structure rearranges. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto: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
