Re: [gmx-users] problem of tabulated bonded potential

On Nov 9, 2010, at 7:12 AM, Z.Xiao wrote: Dear all gmxers, I meet some problems when I use the tabulated bonded potential. My original function is a sum of An*cos(x)^n (n=1-8).For short here I replaced it by cos(x). if f(x)=cos(x),then -f'(x)=sin(x).and the numberical derivative -

Re: [gmx-users] error in editconf step

On 9/11/2010 5:03 PM, vinothkumar mohanakrishnan wrote: Hi try the below command. in your command you have _d in the editconf which is unnecessary. hope it works It's unnecessary to have installed a double-precision version of editconf, but it's not wrong to use it (especially if there is no

[gmx-users] Reg:Density Profile

Hi all, I have a system composed of DCE and Water in a 2.17x2.17x4.9800 simulation box with an dce-water interface.I want to investigate the density profile of the system, and I used the following command line to do that: g_density -f traj.xtc -n index.ndx -dens number -sl 100 The density

Re: [gmx-users] add a group to an amino acid

Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE I finally defined a residue BOC in opls .rtp file: [ BOC ] [ atoms ] N

Re: [gmx-users] add a group to an amino acid

On 9/11/2010 8:19 PM, hengame fallah wrote: Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE So that probably means

Re: [gmx-users] add a group to an amino acid

Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 HA2 BOC 3

Re: [gmx-users] add a group to an amino acid

On 9/11/2010 9:09 PM, hengame fallah wrote: Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540

Re: [gmx-users] add a group to an amino acid

This is .rtp for [PHE] in opls: [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CG

[gmx-users] Installing gromacs in Red hat E5

Dear all, Can anybody tell me the the specification of installation of gromacs 4.5.1 in Red Hat E5 platform. GCC package works good here or any other option I have to think of. Thank you kamalesh Roy Department of Biophysics, Molecular Biology and Bioinformatics University of Calcutta, India --

Re: [gmx-users] problem with g_density

vinothkumar mohanakrishnan wrote: Hi all I also faced a similar problem like Ozge Engi when i used the g_density command for water-DCE interface. when i saw the final .gro file in VMD i saw some 20-25 molecules of water came on one side (end of DCE side) of the box and few molecules of

[gmx-users] problem with g_density

vinothkumar, The roughness of the interface that Justin is suggesting is only one possible explanation for this feature. The other possible explanation is that you are running a NPT simulation and your volume fluctuations are causing the Z-dimension to fluctuate. In this case, g_density

[gmx-users] Re: problem of tabulated bonded potential

XAvier, thanks for your reply. the numberical derivative -f'(n)=dy/dx=-(y(n+1)-y(n-1))/(n+1)-(n-1). so -f'(n)=-(y(n+1)-y(n-1))/2. Is it wrong? On Nov 9, 2010, at 7:12 AM, Z.Xiao wrote: Dear all gmxers, I meet some problems when I use the tabulated bonded potential. My original function is a

Re: [gmx-users] Re: problem of tabulated bonded potential

On Nov 9, 2010, at 1:35 PM, Z.Xiao wrote: XAvier, thanks for your reply. the numberical derivative -f'(n)=dy/dx=-(y(n+1)-y(n-1))/(n+1)-(n-1). so -f'(n)=-(y(n+1)-y(n-1))/2. Is it wrong? Depends on how your x is varying. On Nov 9, 2010, at 7:12 AM, Z.Xiao wrote: Dear all gmxers, I meet

Re: [gmx-users] Installing gromacs in Red hat E5

On 9/11/2010 10:17 PM, Kamalesh Roy wrote: Dear all, Can anybody tell me the the specification of installation of gromacs 4.5.1 in Red Hat E5 platform. GCC package works good here or any other option I have to think of. Thank you kamalesh Roy Department of Biophysics, Molecular Biology and

Re: [gmx-users] add a group to an amino acid

On 9/11/2010 10:10 PM, hengame fallah wrote: This is .rtp for [PHE] in opls: ...wherein all the charge groups are neutral, unlike yours for BOC. This will be fairly moot for a PME simulation, however. [ PHE ] [ atoms ] N opls_238

Re: [gmx-users] problem with g_density

chris.ne...@utoronto.ca wrote: vinothkumar, The roughness of the interface that Justin is suggesting is only one possible explanation for this feature. The other possible explanation is that you are running a NPT simulation and your volume fluctuations are causing the Z-dimension to

[gmx-users] problem with g_density

Is it though? There were actually two problems in g_density. I saw the list of fixes previously and it only says Fixed normalization of g_density using only the last frame. To me, this reads like somebody fixed the most trivial problem (now dividing by the NPT averaged volume instead of

[gmx-users] mdrun in gmx 4.5.1: how to reprogram periodic boundary conditions?

Hi, I'd like to modify how the periodic boundary conditions are implemented when simulating a box with mdrun (the md integrator). Specifically, with two lipid bilayer membranes in the box, I'd like to make it possible for water molecules to move from the space between the membranes to the space

Re: [gmx-users] mdrun in gmx 4.5.1: how to reprogram periodic boundary conditions?

On 10/11/2010 1:32 AM, Adam Herbst wrote: Hi, I'd like to modify how the periodic boundary conditions are implemented when simulating a box with mdrun (the md integrator). Specifically, with two lipid bilayer membranes in the box, I'd like to make it possible for water molecules to move from

Re: [gmx-users] Exclude the 1-2 and 1-3 interactions

Nilesh Dhumal wrote: Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to exclude the 1-2 and 1-3 interactions for solute. I am using OPLS force fild (Gromacs version 4.0.5). If it's diatomic, what 1-3 interactions can it have? Set nrexcl in

Re: [gmx-users] Installing gromacs in Red hat E5

I'd also suggest to install the newest version 4.5.2. Chris 2010/11/9 Kamalesh Roy roy.kamales...@gmail.com Dear all, Can anybody tell me the the specification of installation of gromacs 4.5.1 in Red Hat E5 platform. GCC package works good here or any other option I have to think of.

[gmx-users] g_hbond

Hi everyone, I ran g_hbond on a trajectory. When g_hbond asks for two groups in the index file, I give: group1: Protein group2: ligand The output .ndx file contains 44 Hbonds. In order to verify my result on each and every Hbond, I ran g_hbond on the same trajectory but this time in my index

[gmx-users] Exclude the 1-2 and 1-3 interactions

Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to exclude the 1-2 and 1-3 interactions for solute. I am using OPLS force fild (Gromacs version 4.0.5). Nilesh -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Exclude the 1-2 and 1-3 interactions

By default, Within a same molecule 1-2 and 1-3 interactions does it get excluded? Nilesh On Tue, November 9, 2010 10:19 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to exclude the 1-2

Re: [gmx-users] Exclude the 1-2 and 1-3 interactions

Nilesh Dhumal wrote: By default, Within a same molecule 1-2 and 1-3 interactions does it get excluded? If nrexcl 2, yes. The default (pdb2gmx) behavior sets nrexcl=3, but you haven't indicated how you generated your topology. -Justin Nilesh On Tue, November 9, 2010 10:19 am, Justin A.

[gmx-users] RE: gro file and topology files

Hi, I was wondering if the order of molecules in topology file and the order of coordinates in gro file have to be same. My files are as follows: gro file: 1624 1B1 C1 22.237 30.408 26.522 1B1 SA2 22.348 30.033 26.829 1B1 P3 22.125 30.102 27.144

Re: [gmx-users] RE: gro file and topology files

Nimesh Jain wrote: Hi, I was wondering if the order of molecules in topology file and the order of coordinates in gro file have to be same. My files are as follows: gro file: 1624 1B1 C1 22.237 30.408 26.522 1B1 SA2 22.348 30.033 26.829 1B1 P3

Re: [gmx-users] RE: gro file and topology files

This [ molecules ] directive is at the end of the topology, right ? I was scared all my simulations went wrong. I have the correct order in molecules directive. [ molecules ] SS1 1 SS2 1 Neutral 536 Positive 137 Negative 71 The particles in gro file are in this order. Thank you!

[gmx-users] Re: GB-polarization

Thanks for the clarification but I can't find anything in the .log or .edr-files that would correspond to the non-polar solvation energy. Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631

Re: [gmx-users] Re: GB-polarization

Christian Mücksch wrote: Thanks for the clarification but I can't find anything in the .log or .edr-files that would correspond to the non-polar solvation energy. I think you have to set sa_algorithm=Ace-approximation for this calculation to be done, and thus written. -Justin

[gmx-users] mpirun

Hello, I am using Metadynamics implemented on gromacs, doing normal one dimentional test on a simple system. I see the results of using only one processor or more than one processors are different. always I use the same tpr starting file, So, is it normal to have different results (in my case

[gmx-users] Fw: mpirun

sorry I forgot to add that the random seed for the velocity is the same in all the tprs and the random seed for the thermostat is also the same. and if I redo the simulation with only one processor, the results are always identical. but not with more than one. Do you think is it due to the

Re: [gmx-users] Fw: mpirun

fahimeh baftizadeh wrote: sorry I forgot to add that the random seed for the velocity is the same in all the tprs and the random seed for the thermostat is also the same. and if I redo the simulation with only one processor, the results are always identical. but not with

[gmx-users] trjconv, pbc and breaking of multiple peptides

Hi, I am doing REMD simulations of multiple homopolymeric peptides in a PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to analyze features of the system that require to use g_gyrate to find out the moments of inertia of the system, for example. I understand g_gyrate

Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

ms wrote: Hi, I am doing REMD simulations of multiple homopolymeric peptides in a PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to analyze features of the system that require to use g_gyrate to find out the moments of inertia of the system, for example. I

[gmx-users] New release: 4.5.2

Dear Gromacs users and developers, A new maintenance release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz. It fixes: * Double precision energy file reading * CHARMM and GB issues * Support for Altivec (PowerPC) with CMake * Running binaries within the

[gmx-users] Re: [gmx-developers] New release: 4.5.3

Ooops! Made a mistake in the subject, it was supposed to be 4.5.3 :) Rossen On 11/9/10 10:39 PM, Rossen Apostolov wrote: Dear Gromacs users and developers, A new maintenance release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz. It fixes: * Double

RE: [gmx-users] g_hbond / lifetime

How would it know the lifetime of any other hydrogen bond? The program does exactly what you tell it to. If you tell it to analyse the hydrogen bonds for a particular group, then that is exactly what it will report back to you. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug

[gmx-users] Re: GB-polarization

But in order to get the complete solvation free energy these calculations for the van der Waals and cavity terms have to be done. So does that mean that the solvation free energy calculated by default without specifying sa_algorithm=Ace-approximation is missing these terms? I thought that the

Re: [gmx-users] Re: GB-polarization

Christian Mücksch wrote: But in order to get the complete solvation free energy these calculations for the van der Waals and cavity terms have to be done. So does that mean that the solvation free energy calculated by default without specifying sa_algorithm=Ace-approximation is missing these

[gmx-users] GFP chromophore topology help

Dear gromacs users: I have constructed the Amber03 force fields parameters (bonds,angles, proper and imporer dihedral.) for the chromophore (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the topology. But after energy minimization of the system, the conformation of the

Re: [gmx-users] GFP chromophore topology help

Ramachandran G wrote: Dear gromacs users: I have constructed the Amber03 force fields parameters (bonds,angles, proper and imporer dihedral.) for the chromophore (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the topology. But after energy minimization of the

[gmx-users] ./mdrun

Hi, I am using the dhfr gpu benchmark with mdrun-gpu:dhfr-solv-RF-2nm.bench. export LD_LIBRARY_PATH=/path to OPENMM lib and cuda lib/ export OPENMM_PLUGIN=/path to OPENMM lib plugins/ it shows: Back Off! I just backed up md.log to ./#md.log.1# Reading file topol.tpr, VERSION

Re: [gmx-users] ./mdrun

Hi, as you output says. It infinite long trajectory. Either set a number of steps (in mdp file or with tpbconf) or set a maximum time with (mdrun -maxh) Roland On Tue, Nov 9, 2010 at 9:03 PM, lin hen cutey...@live.com wrote: Hi, I am using the dhfr gpu benchmark with

Re: [gmx-users] multiplicity for qmmm simulations

Hi Jorge, Sorry, I missed you mail earlier. As per the distributed qmmm version, part of the QM information are being fed through the Gromacs mdp file and part through the CPMD_inp.tmpl file. Please specify your QM charge and multiplicity in the CPMD_inp.tmpl file. P.Biswas On Sun, Oct 24,