[gmx-users] Advanced Simulation Analysis

these can not be atom doublet. Has anyone tried that tutorial? Best, Simon Sham -- 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! Pl

[gmx-users] SO4 ion

. Thanks for your help. Simon Sham -- 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

[gmx-users] 2 Questions

Hi, I) I have been trying to figure out where is the source of the following warning message coming from: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom t

[gmx-users] g_rmsf

calculated structures with energy minimization. Do people do the same thing when they average their structures within a certain time period with g_rmsf or g-covar. Thanks for your insight. Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] SO4

program gave the following warnings for the SO42 topology:   WARNING: 'SO42' not found in residue topology database, trying to use 'SO42-' FYI, I use 4.5.1 version. Did I do something wrong in the pdb file? Can I ignore the warning message in #3? Thanks for you help in ad

[gmx-users] g_energy -ravg option

, but not the running averages. Any help is appreciated in advance. Simon Sham -- 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

[gmx-users] g_chi

dihedral angle? Thanks for your help in advance. Simon Sham -- 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

[gmx-users] g_chi

of xmgrace files for each residue, but it does not give a residue #. In the chi.log file, it only listed the four omega atom numbers for each residue...that's it. Again thanks for your help in advance. Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

[gmx-users] g_cluster warning message

atrix 5001 Energy of the matrix is 204.264 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0481586 Linking structures ** Sorting and renumbering clusters What is that rmsd minimum 0 all about? Thanks for your help in advance. Simon Sham -- gmx-users mailing listgmx-users@gromac

[gmx-users] g_saltbr

Hi, I am curious how the donor and acceptor atoms are picked with g_saltbr. For examples, with Asp, it picked CG instead of the two ODs, and with LYS, it picked  CE instead of NZ. Why? Thanks for your help in advance. Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] X-ray Structures

Hi, I have a question about using X-ray PDB files for simulations: 1. Is there any rule of thumb on how good a resolution is required for simulations? I know it has nothing to do with GROMACS. Thanks for your insight. Simon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

[gmx-users] Rg

Hi, I have a question of using Radius of Gyration to analyze my simulation data for a protein at a temperature that it would unfold. My understanding is that when a protein in an unfolded state, it still have some structure and is not a random coil. So, my question is: Will the Rg value for a unf

[gmx-users] Helix to coil

Hi, Does anyone know the time scale for helical to random coil transition? I have done one simulation and noticed that one helical turn of a helix in the crystal structure becomes a loop in the simulation. Have anyone seen something like this before? Best, Simon -- gmx-users mailing list

[gmx-users] oplsaa vs. charmm

Hi, I have recently done two simulations on a protein at high temperature near its melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA to double check the results. There are some differences in the structures between the forcefield used.  I know different forcefields

Re: [gmx-users] oplsaa vs. charmm

Justin has suggested, I probably will try to make a longer run to see what will happen. Best, Simon --- On Fri, 5/27/11, Peter C. Lai wrote: From: Peter C. Lai Subject: Re: [gmx-users] oplsaa vs. charmm To: "simon sham" Cc: "gmx-users@gromacs.org" Date: Friday, May 27, 2011,

[gmx-users] g_helix and g_rotacf

Hi, I have two questions about using g-helix and g_rotacf On g_helix, 1. I have used the following command:     "g_helix -s md.tpr -f md.xtc -n index.ndx -b 1 -e 2"     In the index file, I have residues 10-20 as my group.     However, when I ran the above command, I did not have the n-ahx.

[gmx-users] Order Parameters

Hi, I have a question on correlating the RMSFs with order paramters derived from g_chi - omega or g_rotacf. Which set of order parameters would correlate well, or should I use, with RMSFs? I used C-alpha for RMSFs. Thanks for your insight. Simon -- gmx-users mailing listgmx-users@gromacs.o

[gmx-users] g_rotacf

Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight.

[gmx-users] CHARMM forcefield

Hi, I have two questions about using the charmm force field. 1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl and fix_top_for_charmm.pl? 2. I got the following note when I tried to do energy minim. with grompp: NOTE 1 [file topol.top]:   The largest charge group con

[gmx-users] g_hbond

Hi, I am little confused about setting up the two groups in g_hbond. 1. Are the two groups corresponding to the donor (N) and the acceptor (O) atoms? I want to measure the lifetime, angle and distance of the triplet N-HO hydrogen bond. Is this the triplet that the manual talks about? Thanks

[gmx-users] g_hbond

Hi, To help clarify my previous g_hbond question, I have these two groups in my index file [ a_100_a_101]  # 100 is N, #101 is H    100 101 [ a_200 ]    # 200 is O    200 when I ran g_hbond, I got "Found 1 donors and 2 acceptors". The part that I don't quite understand is why it

[gmx-users] The RMSD of a metal ion

Hi, I would like to look at the positions of a metal ion in MD relative to its original crystal position. I tried g_rms, and I got the following message: "Fatal error : Need >= 3 points to fit" Did I use the correct command to achieve this task? Thanks for your insight in advance. Simon -- g

[gmx-users] pdb2gmx

Hi, I have a question about pdb2gmx. If a pdb file contains a multiple structures, will it average the coordinates or just pick one of the structures to convert? Thanks for your insight. Simon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Metal Ion Position

Hi, I have a question on how to calculate the metal ion position in a protein in a simulation. To be more more specific, I would like to make sure the metal ion stay in the binding site throughout the simulation, and not sure which analysis function to use. I have tried g_rms, and did not work

[gmx-users] Adding Ions

Hi, I have tried to add NaCl into my system in the 4.5.1 version to balance the total charge, and used OPLS forcefield. In the topol file file, it has CL- but no NA+. However, when I ran grompp_d, it gave me the following error message: Program grompp_d, VERSION 4.5.1 Source code file: toppush.c

[gmx-users] Re: Adding Ions

Hi, I have figured the problem. Can't use NA+/CL- in the latest version, and have to use NA/CL at least in OPLS.   Best,   Simon   -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] GROMACS 4.5.1 and MPI

Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I got all sorts of error message such as "opt/apps/gromacs/gromacs-4.5.

[gmx-users] MPI

sistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

[gmx-users] Re: MPI

 OPENMPI?   Thanks in advance,   Simon Sham  Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with &qu

[gmx-users] MPI and dual-core laptop

error: Cannot compile and link MPI code with mpicc" mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- gmx-users ma

[gmx-users] Re: MPI and dual-core laptop

Hi, I was finally able to get my MPI GROMACS running on my laptop. Thanks for all those who have provided invaluable suggestions.    Best,   Simon Sham  --- On Mon, 9/27/10, simon sham wrote: From: simon sham Subject: MPI and dual-core laptop To: gmx-users@gromacs.org Date: Monday, September

[gmx-users] Missing Amino Acids

Hi, 1. I have a protein which is missing both the first and last amino acids in the sequence. Do you know any free linux softwares that can insert these missing amino acids? 2. Since only two amino acids are missing, one in both end, can I simply ignore them in simulations? Thanks for your insi

[gmx-users] Protein in a solvated box

Hi, I have protein in a solvated box. When I used VMD to look at the system, I've found that the protein is not located at the center, but rather at the corner section. I would like to know why. Thanks for your insight in advance. Simon -- gmx-users mailing listgmx-users@gromacs

[gmx-users] High Temperature simulations

Hi, Is it possible to run simulations at high temperatures? Is there any concern in dealing with the solvent water molecules when running high temperature simulations? Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] Error Messages

size of 1.025 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition What does the error message mean? Thanks for your help. Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Langevin Dynamic "bd-temp" parameter

Hi, I tried to run a md calculation with a "bd-temp = 300" line in my file, but it gave a warning: "Unknown left-hand 'bd-temp' in a parameter file" Did I use the right parameter for setting up the temperature in Langevin Dynamics? Thanks for you

[gmx-users] FFTW

Hi, I have tried to install GROMACS in my Slackware linux box. I have fftw 3. something installed separatedly. However, when I configured GROMACS, the fft3 headers were found but not the library files. They are located in /usr/local/include and /usr/local/lib respectively. I also tried to config