RE: [gmx-users] NVT equilibration
Are you running NVT with position restraint dynamics of your protein? Your system is probably not minimizied enough. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, August 09, 2012 1:23 PM To: Discussion list for GROMACS users Subject: [gmx-users] NVT equilibration Dear gmx users, I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error: Fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? Cheers, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation
Those tutorials show most important things (e.g. how to build topology for given system) in CG Martini ff using Gromacs. You do not have to merge anything. Commands are the same as for atomistic simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of J Peterson [think_bey...@aol.com] Sent: Tuesday, August 07, 2012 5:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the available Martini files and programs with the recent version of GROMACS that is version 4? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p486.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] tutorials for Coarse-Grained MD Simulation
For MARTINI force field: http://md.chem.rug.nl/cgmartini/index.php/tutorial Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of J Peterson [think_bey...@aol.com] Sent: Monday, August 06, 2012 6:41 AM To: gmx-users@gromacs.org Subject: [gmx-users] tutorials for Coarse-Grained MD Simulation Dear Gromacs Users, I would like to know if there are any tutorials for Coarse-Grained MD Simulation available anywhere. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] place carbon nanotube along the z direction
You can use editconf -princ to orient it into the principal axis. Then with editconf -rotate specify proper vector of 90 degrees if required. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Abed Askari [abedask...@yahoo.com] Sent: Friday, August 03, 2012 1:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] place carbon nanotube along the z direction Dear gmx-users I would like to orient my carbon nanotube along the z direction. would you please tell me how I can do that?Do I use any option other than -box when I use editconf or something?my command was editconf -f cnt.pdb -o cnt.gro -box 5 5 5 any help would be really appreciated. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] to know about constraints
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Wednesday, June 20, 2012 8:24 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] to know about constraints Hello Justin For freezefprs, am using the .mdp file as follows: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N . The error file is coming as: Fatal error: Invalid Freezing input: 2 groups and 2 freeze values Is the .mdp wrong please suggest Specify index file which include those two groups (K+ C-) with those names. You should also specify the third dimension for each group I guess: freezedim = N N Y N N Y From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, June 20, 2012 12:09 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 6/19/12 2:35 PM, Anik Sen wrote: Hello Justin, This is Anik again. I checked the links. But could not understand fully. Am giving the part of the topology file as given below, generated with the command pdb2gmx -f a.pdb -o b.pdb -p topol.top The topology file : 205CL-205CL- Cl205 -1 35.453 ; qtot 35 206CL-206CL- Cl206 -1 35.453 ; qtot 34 207CL-207CL- Cl207 -1 35.453 ; qtot 33 208CL-208CL- Cl208 -1 35.453 ; qtot 32 209CL-209CL- Cl209 -1 35.453 ; qtot 31 210CL-210CL- Cl210 -1 35.453 ; qtot 30 211CL-211CL- Cl211 -1 35.453 ; qtot 29 212CL-212CL- Cl212 -1 35.453 ; qtot 28 213CL-213CL- Cl213 -1 35.453 ; qtot 27 214CL-214CL- Cl214 -1 35.453 ; qtot 26 215CL-215CL- Cl215 -1 35.453 ; qtot 25 216CL-216CL- Cl216 -1 35.453 ; qtot 24 217CL-217CL- Cl217 -1 35.453 ; qtot 23 218CL-218CL- Cl218 -1 35.453 ; qtot 22 219CL-219CL- Cl219 -1 35.453 ; qtot 21 220CL-220CL- Cl220 -1 35.453 ; qtot 20 221CL-221CL- Cl221 -1 35.453 ; qtot 19 222CL-222CL- Cl222 -1 35.453 ; qtot 18 223CL-223CL- Cl223 -1 35.453 ; qtot 17 224CL-224CL- Cl224 -1 35.453 ; qtot 16 225CL-225CL- Cl225 -1 35.453 ; qtot 15 226CL-226CL- Cl226 -1 35.453 ; qtot 14 227CL-227CL- Cl227 -1 35.453 ; qtot 13 228CL-228CL- Cl228 -1 35.453 ; qtot 12 229CL-229CL- Cl229 -1 35.453 ; qtot 11 230CL-230CL- Cl230 -1 35.453 ; qtot 10 231CL-231CL- Cl231 -1 35.453 ; qtot 9 232CL-232CL- Cl232 -1 35.453 ; qtot 8 233CL-233CL- Cl233 -1 35.453 ; qtot 7 234CL-234CL- Cl234 -1 35.453 ; qtot 6 235CL-235CL- Cl235 -1 35.453 ; qtot 5 236CL-236CL- Cl236 -1 35.453 ; qtot 4 237CL-237CL- Cl237 -1 35.453 ; qtot 3 238CL-238CL- Cl238 -1 35.453 ; qtot 2 239CL-239CL- Cl239 -1 35.453 ; qtot 1 240CL-240CL- Cl240 -1 35.453 ; qtot 0 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include tip4p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif This includes the posre.itp as follows: ; In this topology include file, you will find position
RE: [gmx-users] to know about constraints
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Wednesday, June 20, 2012 10:20 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] to know about constraints Dear Mark, In the section it is written that : freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid SOL). freezedim specifies for which dimension the freezing applies. To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that frozen coordinates are not subject to pressure scaling. freezedim:dimensions for which groups in freezegrps should be frozen, specify Y or N for X, Y and Z and for each group (e.g. Y Y N N N N means that particles in the first group can move only in Z direction. The particles in the second group can move in any direction). I have also made the .mdp file accordingly as follows: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N energygrp_excl = Cl- SOL K+ SOL ;dt = 0.0005 ; ps ! dt = 0.0005 ; ps ! nsteps = 20 - - THIS IS WRONG! It should be: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N Y N N Y energygrp_excl = Cl- SOL K+ SOL ;dt = 0.0005 ; ps ! dt = 0.0005 ; ps ! nsteps = 20 so K+ can move only in Y and CL- can move only in Y direction. When you grompp use index file (-n index.ndx) with names of those groups: K+ CL- corresponding to proper atoms. But still the similar error arises. Fatal error: Invalid Freezing input: 2 groups and 2 freeze values ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Wednesday, June 20, 2012 1:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 20/06/2012 5:24 PM, Anik Sen wrote: Hello Justin For freezefprs, am using the .mdp file as follows: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N . The error file is coming as: Fatal error: Invalid Freezing input: 2 groups and 2 freeze values Look at the requirements for freeze groups in manual section 7.3... Mark Is the .mdp wrong please suggest From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, June 20, 2012 12:09 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 6/19/12 2:35 PM, Anik Sen wrote: Hello Justin, This is Anik again. I checked the links. But could not understand fully. Am giving the part of the topology file as given below, generated with the command pdb2gmx -f a.pdb -o b.pdb -p topol.top The topology file : 205CL-205CL- Cl205 -1 35.453 ; qtot 35 206CL-206CL- Cl206 -1 35.453 ; qtot 34 207CL-207CL- Cl207 -1 35.453 ; qtot 33 208CL-208CL- Cl208 -1 35.453 ; qtot 32 209CL-209CL- Cl209 -1 35.453 ; qtot 31 210CL-210CL- Cl210 -1 35.453 ; qtot 30 211CL-211CL- Cl211 -1 35.453 ; qtot 29 212CL-212CL- Cl212 -1 35.453 ; qtot 28 213CL-213CL- Cl213 -1 35.453 ; qtot 27 214CL-214CL- Cl214 -1 35.453 ; qtot 26 215CL-215CL- Cl215 -1 35.453 ; qtot 25 216CL-216CL- Cl216 -1 35.453 ; qtot 24 217CL-217CL- Cl217 -1 35.453 ; qtot 23 218CL-218CL- Cl218 -1 35.453 ; qtot 22 219CL-219CL- Cl219 -1 35.453 ;
RE: [gmx-users] to know about constraints
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Marzinek, Jan [j.marzine...@imperial.ac.uk] Sent: Wednesday, June 20, 2012 10:30 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] to know about constraints From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Wednesday, June 20, 2012 10:20 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] to know about constraints Dear Mark, In the section it is written that : freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid SOL). freezedim specifies for which dimension the freezing applies. To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that frozen coordinates are not subject to pressure scaling. freezedim:dimensions for which groups in freezegrps should be frozen, specify Y or N for X, Y and Z and for each group (e.g. Y Y N N N N means that particles in the first group can move only in Z direction. The particles in the second group can move in any direction). I have also made the .mdp file accordingly as follows: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N energygrp_excl = Cl- SOL K+ SOL ;dt = 0.0005 ; ps ! dt = 0.0005 ; ps ! nsteps = 20 - - THIS IS WRONG! It should be: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N Y N N Y energygrp_excl = Cl- SOL K+ SOL ;dt = 0.0005 ; ps ! dt = 0.0005 ; ps ! nsteps = 20 so K+ can move only in Y and CL- can move only in Y direction. When you grompp use index file (-n index.ndx) with names of those groups: K+ CL- corresponding to proper atoms. Sorry in Z direction! If you want to freeze two groups in all directions: freezedim = N N N N N N But still the similar error arises. Fatal error: Invalid Freezing input: 2 groups and 2 freeze values ___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Wednesday, June 20, 2012 1:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 20/06/2012 5:24 PM, Anik Sen wrote: Hello Justin For freezefprs, am using the .mdp file as follows: ; title = NACL6 cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep freezegrps = K+ CL- freezedim = N N . The error file is coming as: Fatal error: Invalid Freezing input: 2 groups and 2 freeze values Look at the requirements for freeze groups in manual section 7.3... Mark Is the .mdp wrong please suggest From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, June 20, 2012 12:09 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 6/19/12 2:35 PM, Anik Sen wrote: Hello Justin, This is Anik again. I checked the links. But could not understand fully. Am giving the part of the topology file as given below, generated with the command pdb2gmx -f a.pdb -o b.pdb -p topol.top The topology file : 205CL-205CL- Cl205 -1 35.453 ; qtot 35 206CL-206CL- Cl206 -1 35.453 ; qtot 34 207CL-207CL- Cl207 -1 35.453 ; qtot 33 208CL-208CL- Cl208 -1 35.453 ; qtot 32 209CL-209CL- Cl209 -1 35.453 ; qtot 31 210CL-210CL- Cl210 -1 35.453 ; qtot 30 211CL-211CL- Cl211 -1 35.453 ; qtot 29 212CL-212CL- Cl212 -1 35.453 ; qtot 28 213CL-213CL- Cl213 -1 35.453 ; qtot 27 214CL-214CL- Cl214 -1 35.453 ; qtot 26 215
RE: [gmx-users] Regarding error
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Seera Suryanarayana [paluso...@gmail.com] Sent: Friday, May 25, 2012 6:23 AM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, While i am using the commond pdb2gmx -f 4E82.pdb -o 4E82.gro -p 4E82.top.I am getting the following warnings and errors. Warning: Residue EME21 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ILE22 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue SER23 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLY24 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ARG25 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue CYS20 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3CYS5 CYS10 CYS20 CYS30 SG18SG36SG75 SG144 SG228 CYS5SG36 0.834 CYS10SG75 0.936 1.000 CYS20 SG144 0.833 0.203 0.935 CYS30 SG228 0.856 0.827 0.200 0.788 CYS31 SG234 0.202 0.860 0.783 0.820 0.734 Linking CYS-3 SG-18 and CYS-31 SG-234... Linking CYS-5 SG-36 and CYS-20 SG-144... Linking CYS-10 SG-75 and CYS-30 SG-228... Start terminus ALA-1: NH3+ End terminus CYS-20: COO- Fatal error: Residue 'EME' not found in residue topology database. http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database Jan Kindly tell me how to over come this error. Suryanarayana Seera, PhD student, Hyderabad, India. -- 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] Chemical Potential
Hi Fabian, The tpi integrator will caluclate it for you when you simply add the extra molecule to your gro and topology: http://www.mail-archive.com/gmx-users@gromacs.org/msg50610.html Best, Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Fabian Casteblanco [fabian.castebla...@gmail.com] Sent: Tuesday, May 22, 2012 11:54 PM To: gmx-users@gromacs.org Subject: [gmx-users] Chemical Potential Hello community, I'm just trying to explore what kind of calculations one can do on polymer systems (pure or in water) in order to validate the force field works accurately for that system. I know there are basics such as density, volume, dH of vaporization, isothermal compressibility, heat capacity, etc. I've been reading about the particle insertion method to calculate chemical potentials. Since the chemical potential is simply the change in gibbs as the number of particles changes, can one use the g_bar method to simply insert/delete a molecule to/from the system? Anybody know an article where this or something similar was done? Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- 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] line longer than 4095 - a bug?
Dear Gmx Users, Many of you probably faced an error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' As I noted this error comes from the changes in the topology. Gromacs somehow add _ and thus this problem occurs. For instance: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 4 5 1 4 6 1 _ 424 1 6 7 1 I could not see _ using vi in my topology. However, when I copied all topology to another text editor I could. Then removing it solves the problem. Is that a bug? This is just to inform people for the future as I have spent many hours to find out what is wrong. Best, Jan -- 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] pullf.xvg
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Krzysztof Kuczera [kkucz...@ku.edu] Sent: Wednesday, May 02, 2012 6:38 PM To: Discussion list for GROMACS users Subject: [gmx-users] pullf.xvg Could someone please tell me what exactly is printed in the pullf.xvg file from an umbrella sampling simulation? Is it the total force acting the COM of the pull group - i.e. force from regular potential plus the umbrella force or just the unbiased force? Krzysztof Kuczera Each window in umbrella sampling simulation gives you the biased potential which is the harmonic potential. The wham allows you to combine all windows by applying weights and calculating the unbiased potential which requires calculation of the free enerrgy associated with introducing the harmonic pontial (biased). Please, search literature to see equations. Jan -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] g_dist explanation
Use trjconv -skip first for your trajcetory so you can rewrite it every frame/time step you want. Then proceed to g_dist. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shilpi Chaurasia [shilpi.chaura...@unimi.it] Sent: Monday, April 23, 2012 3:59 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_dist explanation Hi Gromacs users, I am using pull code to separate two units of a protein dimer. I have run the pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the data is printed at every 0.01 ps (according to pull_nstxout pull_nstfout, both are 10 in this case) as given below 0. 0.000322052 0.0100 0.173534 0.0200 0.297454 0.0300 0.416585 0.0400 0.519195 0.0500 0.597541 ... Now, I want to calculate the distance between COM of two groups using g_dist and printing the output data in the same time steps as in .xvg files. I tried but the output data is printed at every 2ps steps as following: 0.0008.0175037 -0.0010343 -0.00555138.0175018 2.0008.0188007 -0.0202498 -0.01143268.0187674 4.0008.0377693 -0.0229554 -0.01298148.0377254 6.0008.0435743 -0.0226321 -0.00432448.0435410 8.0008.0615864 -0.0312104 -0.01166828.0615177 ... command used g_dist -f *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650 I have also tried by using different values for 'dt' but it doesn't help. If someone could tell me how to control the time steps in g_dist output, in this case I want the output to be printed in the steps of 0.01 ps thanks, Shilpi -- 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] g_dist explanation
But the best would be to grompp (NPT) windows (lets say every 10-20 frames) of your configuration and at the end of grompp you will see the actual distance the gromacs will consider. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shilpi Chaurasia [shilpi.chaura...@unimi.it] Sent: Monday, April 23, 2012 3:59 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_dist explanation Hi Gromacs users, I am using pull code to separate two units of a protein dimer. I have run the pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the data is printed at every 0.01 ps (according to pull_nstxout pull_nstfout, both are 10 in this case) as given below 0. 0.000322052 0.0100 0.173534 0.0200 0.297454 0.0300 0.416585 0.0400 0.519195 0.0500 0.597541 ... Now, I want to calculate the distance between COM of two groups using g_dist and printing the output data in the same time steps as in .xvg files. I tried but the output data is printed at every 2ps steps as following: 0.0008.0175037 -0.0010343 -0.00555138.0175018 2.0008.0188007 -0.0202498 -0.01143268.0187674 4.0008.0377693 -0.0229554 -0.01298148.0377254 6.0008.0435743 -0.0226321 -0.00432448.0435410 8.0008.0615864 -0.0312104 -0.01166828.0615177 ... command used g_dist -f *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650 I have also tried by using different values for 'dt' but it doesn't help. If someone could tell me how to control the time steps in g_dist output, in this case I want the output to be printed in the steps of 0.01 ps thanks, Shilpi -- 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] Gromos87
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, April 12, 2012 4:05 PM To: Discussion list for GROMACS users Subject: [gmx-users] Gromos87 Dear friends, I'd like to use gormos87 force field in my simulation. Which force field am I supposed to select? 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR Thanks in advance, Shima No clue why do you want to use this force field which is an old version. Would you like to reproduce some results? Download it and copy to your folder where you use pdb2gmx. It will appear as the first option then. Jan -- 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] Gromos87
From: Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, April 12, 2012 4:53 PM To: Marzinek, Jan Subject: Re: [gmx-users] Gromos87 Dear Jan, I downloaded the file and put it in my working space but does not appear in my force filed selections? How come? What's wrong with it? Cheers, Shima You should have downloaded not a single file but the whole force field which is a folder and the copy it to the directory you working in. As Felix mentioned it could be number: 17: [DEPRECATED] Gromacs force field (see manual) so you do not have to download it. Ensure this is a version you need. Jan From: Marzinek, Jan j.marzine...@imperial.ac.uk To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, April 12, 2012 7:42 PM Subject: RE: [gmx-users] Gromos87 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, April 12, 2012 4:05 PM To: Discussion list for GROMACS users Subject: [gmx-users] Gromos87 Dear friends, I'd like to use gormos87 force field in my simulation. Which force field am I supposed to select? 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR Thanks in advance, Shima No clue why do you want to use this force field which is an old version. Would you like to reproduce some results? Download it and copy to your folder where you use pdb2gmx. It will appear as the first option then. Jan -- 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] on -t nvt.cpt in the Justine Lemkul tutorial
Well... There is no mistake as for the option -t of grompp in the suggested version for this tutorial the file can be both trajcetory (trr) or a checkpoint file (cpt) from previous NVT ensemble. I hope you understand what you are doing? Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Acoot Brett [acootbr...@yahoo.com] Sent: Monday, March 19, 2012 9:19 AM To: Discussion list for GROMACS users Subject: [gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial Dear All, I am using the GROMACS 3.3.3 to practice the lysozyme tutorial of Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html. For the final part grompps, for example grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr, it shows the nvt.cpt.trr. cannot be read. Then I change grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr into grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -o npt.tpr, it works. I am looking a clarification from you that my change is correct. Cheers, Acoot -- 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] em.mdp file
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Lara Bunte [lara.bu...@yahoo.de] Sent: Monday, March 05, 2012 5:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] em.mdp file Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 Thanks for help Greetings Lara This file is for energy minimization rather than for a MD run. Start reading Manual together with Justin's tutorials to clarify the basics: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ Jan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] error
try: $ df -h . And see how much quota you have available. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of RAMYA NAGA [nagra...@gmail.com] Sent: Wednesday, February 29, 2012 8:28 AM To: Discussion list for GROMACS users Subject: [gmx-users] error Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me how to solve this error -- Ramya.LN -- Ramya.LN -- 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] HBonds with VMD
Try the representation: all not water Then set it to the HBONDS And refer to the VMD mailing list next time! :) Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, February 24, 2012 9:50 PM To: Hovakim Grabski; Discussion list for GROMACS users Subject: Re: [gmx-users] HBonds with VMD Hovakim Grabski wrote: Dear GROMACS users, I'm a novice user, I've been trying to find a way to visualize hydrogen bonds with VMD,but I haven't been successful. After running a simulation of 13 Hypericin molecules solved in Water, I loaded the.gro file and then the trajectory file .xtc, after that in the Create Representation window I changed to CPK and then modified to show just the Hypericin molecules (not water).Later I created another representation and changed to HBONDS and in the panel changed to name H O,but VMD doesn't show the HBONDS formed between O and H atoms. Where is my mistake? Probably the atom names are wrong. This is a VMD question, so you're better off posting to the VMD mailing list for help on such topics. -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 -- 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] HBonds with VMD
Dear GROMACS users, I'm a novice user, I've been trying to find a way to visualize hydrogen bonds with VMD,but I haven't been successful. After running a simulation of 13 Hypericin molecules solved in Water, I loaded the.gro file and then the trajectory file .xtc, after that in the Create Representation window I changed to CPK and then modified to show just the Hypericin molecules (not water).Later I created another representation and changed to HBONDS and in the panel changed to name H O,but VMD doesn't show the HBONDS formed between O and H atoms. Where is my mistake? Thanks in Advance Hovakim Grabski Russian-Armenian(Slavonic) University I think you should refer to VMD mailing list. However, as far as I know you should create representation: all not water and set to HBONDS Jan -- 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] multi file input for index files
So as you can see Gromacs does not support multi file input :) Create one index file and specify there your two groups. Then g_hbond will ask you to choose two groups from this file. Jan === Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.ukmailto:j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@gmail.com] Sent: Tuesday, January 10, 2012 8:13 AM To: Discussion list for GROMACS users Subject: [gmx-users] multi file input for index files Dear users, I created two different index files (A.ndx and B.ndx). I want to run the two files at the same time. e.g. g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx where, I want to calculate the hydrogen bonds between A and B. This command is giving the error as it expected. Gromacs tools do not support multi file input for index files from http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. Is this correct? If no, what should I do? Thanks in advance -- Ahmet Yıldırım -- 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] trjconv and -pbc
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, while this small molecular outside, I did not meet such issue before, it's used to be easy to fix the pbc problem, but not this one. a bit surprise, They are supposed to be together, Thanks for any advice, I am sure it will help. Follow the workflow! http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc Just use the trjconv -h to see each option. Jan === Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 -- 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] PRODRG topology
Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this? Thank you in advance, Jan -- 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] EM - Starting point on the hypersurface
Dear Gromacs Users, As I know for the Energy Minimization algorithms both Steepest Descent and Conjugate Gradient will not provide a global minimum of the potential energy but only a local minium. Does anyone know how Gromacs choose the starting point on the potential energy hypersurface for the beginning of Energy Minimization? Thank you in advance, Jan Marzinek -- 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] SAS of ligands
Dear Gromacs Users, My system has 30 ligands - they aggregate and and seperate during the simulation time and stack to two sites of my protein (two clusters). I want to calculate the interface area between ligands and protein so I need to substract the interface between ligands due to the aggregations. Do you know how to do this? Thank you in advance! Jan -- 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] SAS of ligands
Dear Justin, Thank you for the link! I know how to calculate it - that is what I am doing. Interface AREA = 0.5 (Protein SAS+ 30 Ligands SAS- Protein and 30Ligands SAS) This is relevant to the situation where ligands do not aggregate. I my system 22 out of 30 ligands bind to my protein creating two clusters on the terminals of the protein. In this case they cover the area between them. What I think is that I have to substract the interface between them from this equation. Am I right? The question is - how to do this? g_cluster will help? Thank you. Jan Marzinek From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Tuesday, July 05, 2011 12:45 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SAS of ligands Marzinek, Jan wrote: Dear Gromacs Users, My system has 30 ligands - they aggregate and and seperate during the simulation time and stack to two sites of my protein (two clusters). I want to calculate the interface area between ligands and protein so I need to substract the interface between ligands due to the aggregations. Do you know how to do this? See the thread from just a few days ago about the same question: http://lists.gromacs.org/pipermail/gmx-users/2011-July/062707.html -Justin Thank you in advance! Jan -- 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
RE: [gmx-users] SAS of ligands
Thank you Justin! From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Tuesday, July 05, 2011 1:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SAS of ligands Marzinek, Jan wrote: Dear Justin, Thank you for the link! I know how to calculate it - that is what I am doing. Interface AREA = 0.5 (Protein SAS+ 30 Ligands SAS- Protein and 30Ligands SAS) This is relevant to the situation where ligands do not aggregate. I my system 22 out of 30 ligands bind to my protein creating two clusters on the terminals of the protein. In this case they cover the area between them. What I think is that I have to substract the interface between them from this equation. Am I right? The question is - how to do this? g_cluster will help? Yes, you do have to account for ligand-ligand interactions and buried surfaces, and I suspect that doing so won't be trivial. Probably lots of iterations of g_sas will be required to cover all the necessary permutations of different interfaces. g_cluster may help, but if you already know that the clusters form it's just a matter of determining which molecules (by residue number) are involved in each cluster so you can make appropriate index groups. -Justin Thank you. Jan Marzinek From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Tuesday, July 05, 2011 12:45 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] SAS of ligands Marzinek, Jan wrote: Dear Gromacs Users, My system has 30 ligands - they aggregate and and seperate during the simulation time and stack to two sites of my protein (two clusters). I want to calculate the interface area between ligands and protein so I need to substract the interface between ligands due to the aggregations. Do you know how to do this? See the thread from just a few days ago about the same question: http://lists.gromacs.org/pipermail/gmx-users/2011-July/062707.html -Justin Thank you in advance! Jan -- 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 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 -- 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] coiled coil unfolding
Dear Gromacs Users, I am running the simualtions between ligands (10-30) and protein - coiled coil segment. My ligand is strongly hydrophobic and the hydrohpohobic strand between two monomers is obviously hidden. I found that my proetin is unfloding from terminals, two strands open allowing ligands to come into hydrophobic residues - the helical structure is partly destroyed as well as coiled coil. That sounds ok in terms of hydrophobicity. However, maybe I should run simulation with constrained backbone and coiled coil? What do you think? Regards, Jan === Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.ukmailto:j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_sas index files/hydrogen bonds
Dear Gromacs Users, I am calculating the hydrophobic interface area using g_sas between ligands (their hydrophobic solvent accessible surface area (SASA) 95%) and hydrophobic residues of coiled coil fragment of protein (two helical strands) as follows: Protein SASA + ligand SASA - ProteinLigand SASA = Interface Area between ligands protein I obtained the hydrophobic interface area increasing during the simulation time - so everything seems to be ok, because from my simulation 10 ligands occupy hydrophobic residues (the helical terminal strands open allowing ligands to come inside the protein). However, 10 ligands aggregates during the simulation covering their hydrophobic surface which obviously has the influence on the final interface between protein and ligands. Do you know how to calculate the interface area between all 10 ligands during the simulation time in order to subtract from final result? How should I define index files? The second question: I also calculated the hydrogen bonds between ligands and the protein. What is interesting: app. 70% of hydrogen bonds between hydrophobic ligands are formed with HYDROPHILIC residues of protein. Any clue what is happening as final conformation involve ligands between hydrophobic surfaces of the protein? All the best, Jan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond/g_sas - how is it calculated?
Hi, I have a question related to the calculation of hydrogen bonds in Gromacs. As I read in Manual it comes from the distance between donor and acceptor ( = 0.35 nm) and the angle =30 degr beween hydrogen and acceptor. The question is - why 30 degr? How is it related to the reality? The second thing is the claculation of the accessible surface area (g_sas) of the molecule for instance? It is not explained in manual and I am really curious how g_sas makes these calculations. As my supervisors do not know the gromacs their questions are always about such details :) However, I think it is really important to understand what you are really doing using commands in Gromacs which provide you with really detailed results. Thank you in advance, Jan -- 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
