[gmx-users] Insertion of chromium III ion into lipid bilayer

Hi, I want to add chromium III ion into lipid bilayer. I have included cr entry in the ions.itp file, and I used grompp it shows error like Atom types cr+3 is not found. After removing cr ions from the ions.itp file it works and after using genion to add cr3+ ions into lipid the following

Re: [gmx-users] Insertion of chromium III ion into lipid bilayer

First, can you successfully add an ion that the force field already knows about, like potassium? Second, does the force field know about chromium? If not, who does? Mark On Sat, Oct 19, 2013 at 4:27 PM, Sathya bti027.2...@gmail.com wrote: Hi, I want to add chromium III ion into lipid

Re: [gmx-users] Insertion of chromium III ion into lipid bilayer

On 10/19/13 10:27 AM, Sathya wrote: Hi, I want to add chromium III ion into lipid bilayer. I have included cr entry in the ions.itp file, and I used grompp it shows error like Atom types cr+3 is not found. After removing cr ions from the ions.itp file it works and after using genion to

[gmx-users] Re: Insertion of chromium III ion into lipid bilayer

Dear Justin, Please Tell me is there any possible option for inserting cr into into DPPC bilayer. -- View this message in context: http://gromacs.5086.x6.nabble.com/Insertion-of-chromium-III-ion-into-lipid-bilayer-tp5011884p5011886.html Sent from the GROMACS Users Forum mailing list archive at

Re: [gmx-users] Re: Insertion of chromium III ion into lipid bilayer

On 10/19/13 11:53 AM, Sathya wrote: Dear Justin, Please Tell me is there any possible option for inserting cr into into DPPC bilayer. Well, anything is possible. You'd have to define an atomtype that represents Cr, which will involve deriving suitable LJ parameters that reproduce some

[gmx-users] Bilayer thickness error

Hi, This is my input file for calculating bilayer thickness in absence of peptide: ## Input file and input file parameters coord_file md.gro file_type gro num_frames 1 num_lipid_types1 resname1POPC atomname1 P8

Re: [gmx-users] Problem with reading AMBER trajectories

Can this file be opened in VMD itself? Mark On Oct 18, 2013 6:21 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few analysis. Unfortunately I ended-up with the following error.

Re: [gmx-users] Bilayer thickness error

On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote: Hi, This is my input file for calculating bilayer thickness in absence of peptide: ## Input file and input file parameters coord_file md.gro file_type gro num_frames 1 num_lipid_types1

Re: [gmx-users] Problem with reading AMBER trajectories

Hi Mark, Yes. I do can able to load the trajectories successfully in VMD with the file format option of ' AMBER coordinate with periodic box'. I am using VMD 1.9 version. Regards Anu On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Can this file be opened in VMD

Re: [gmx-users] Bilayer thickness error

thank you so much. It was such a stupid error from my side. On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote: Hi, This is my input file for calculating bilayer thickness in absence of peptide: ## Input file and

Re: [gmx-users] Problem with reading AMBER trajectories

OK. All GROMACS does is feed your filename extension to the VMD library and let it choose how to read the file based on that. If that doesn't make sense (and it seems it doesn't, because GROMACS wasn't told about the number of atoms, and it needs to know), then the ball is back to you to choose

[gmx-users] modification of LJ potential

Dear GROMACS users,I went through the mailing list but I am still not sure about my problem. I am going to simulate two chains in a tube using GROMACS. The chains are modeled as strings of connected beads and I would like to describe the interaction with the tube aligned with z axis and passing

[gmx-users] Molecular dynamics with LEGO?

Hi :) Apologies if this seems inappropriate, but I would like to ask as many people as I can to give support for the molecular modeling LEGO project at http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will consider producing the bricks required for such models, and we can add cool

Re: [gmx-users] Molecular dynamics with LEGO?

Hi Tsjerk, In my opinion, we don't need to develop LEGO specifically for this - something already exists, which I played with in school. The molymod pieces (http://www.molymod.com/) already include bendy pieces, which are the next step on the lego website you advertise. Best wishes James Hi :)

Re: [gmx-users] Molecular dynamics with LEGO?

Hi James, There are models, yes. But if a manufacturer like LEGO is taking this up, it can make the models much cheaper and more easily available. In addition, the LEGO models would allow more flexibility in building and handling. And you can combine it with your other LEGO ;) And, yes, bendy

[gmx-users] mistake occured in Gromacs install

Dear professor: When I install the Gromacs software, there occured a problem as follow(my computer is 64bit,linux, gcc is GNU Fortran (GCC) 4.6.2): [ZHP@console build]$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -- No compatible CUDA toolkit found (v3.2+), disabling native GPU acceleration CMake

Re: [gmx-users] mistake occured in Gromacs install

You do need a C compiler, not a Fortran one, and IIRC gcc 4.6.2 has some known issues. Please follow the instructions in the install guide and get the latest compiler you can. Mark On Oct 17, 2013 8:30 AM, 张海平 21620101152...@stu.xmu.edu.cn wrote: Dear professor: When I install the Gromacs

[gmx-users] Free energy of solvation of large molecule

Hi, I'm trying to calculate the free energy of solvation of a relatively large polymer molecule (161 atoms). I went through the free energy tutorial published on J. Lemkul's web page but when trying to apply the same approach to my case, the simulations typically fail. The files for one such

Re: [gmx-users] default -rdd with distance restraints seems too large

Hi, The log file gives a breakdown of how the minimum cell size was computed. What does it say? Mark On Oct 17, 2013 5:17 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: I have a system that also uses a set of distance restraints The box size is: 7.12792 7.12792 10.25212

Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

4.5 can only handle about 500-1000 atoms per processor. Details vary. Mark On Oct 17, 2013 5:39 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Thanks for you reply. I am doing simulation for ionic liquids BMIM + CL. Total number of atoms are 3328. Nilesh Assuming you're using LINCS,

[gmx-users] lipid tail order

Hi, I want to plot 1. -SCD (lipid tail order parameters) profile for both the chains (sn1 and sn2) 2. Lateral diffusion of lipids 3. density profiles in presence and absence of peptide. I have plotted the above parameters in presence of peptide, for calculating in absence of peptide, do i

[gmx-users] postdoctoral position in computational biophysics in Denmark

A postdoctoral position in simulations of membranes and membrane proteins is available from 1 December 2013 (starting date flexible) for one year (with possible extension) at the University of Southern Denmark (SDU), Odense in the group of Dr Himanshu Khandelia. Knowledge of statistical physics

Re: [gmx-users] Is the website of Martini Force Field down for maintenance?

Try cgmartini.nl On Oct 16, 2013, at 10:29 PM, 朱文鹏 jasonzhu...@gmail.com wrote: Dear GMX users, I am going to do some coarse-grained simulations in which the lipid bilayeris covered by polysarccharide. I remember the website of Martini Force Field (http://md .chem.rug.nl/cgmartini/)

[gmx-users] (no subject)

Hi, Please tell me what is wrong in my input file. I am not getting APL along with std deviation values. Following is the input and output for calculating APL Input file coord_file md.gro file_type gro num_frames1 num_lipid_types 1 resname1

Re: [gmx-users] lipid tail order

On 10/17/13 4:57 AM, Archana Sonawani-Jagtap wrote: Hi, I want to plot 1. -SCD (lipid tail order parameters) profile for both the chains (sn1 and sn2) 2. Lateral diffusion of lipids 3. density profiles in presence and absence of peptide. I have plotted the above parameters in presence

Re: [gmx-users] MD of lipid bilayer

On 10/16/13 10:32 PM, Sathya wrote: Dear Justin, I am currently working on Dynamics study of DPPC lipid bilayer and chromium ions.. I want to know how to insert chromium ions into lipid bilayer. Is there any software for this? Please suggest some idea about how to

[gmx-users] parallelization

Dear gromacs users I would like to run my simulations on all nodes(8) with full utilisation of all cores(2 each). I have compiled gromacs version 4.6.3 using both thread mpi and open mpi. I am using following command: mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro But I am getting following

Re: [gmx-users] parallelization

Hi, On Oct 17, 2013, at 2:25 PM, pratibha kapoor kapoorpratib...@gmail.com wrote: Dear gromacs users I would like to run my simulations on all nodes(8) with full utilisation of all cores(2 each). I have compiled gromacs version 4.6.3 using both thread mpi and open mpi. I am using following

[gmx-users] default -rdd with distance restraints seems too large

Indeed, sorry that I didn't notice that, Mark. Looks as if the two-body bonded interaction gets multiplied by 1.1/0.8 so I suppose that this is working as it should. It's a shame that long distance restraints limit the parallalization so much, but it is understandable. Thanks for helping me

Re: [gmx-users] default -rdd with distance restraints seems too large

Yes it is a pity! But particle decomposition helps :)) well helped! It's a shame that long distance restraints limit the parallalization so much, but it is understandable. Thanks for helping me with this. Chris. -- original message -- Initializing Domain Decomposition on 8 nodes

[gmx-users] default -rdd with distance restraints seems too large

Thanks for the hint XAvier. Unfortunately, I get crashes with particle decomposition (see below). If I use either DD or PD, I can run on up to 2 threads without adjusting -rdd or -dds. I can only use 2 thread with DD if I set -rdd 2.8. If I try to use more than 2 threads with PD, I get lincs

Aw: [gmx-users] g_sham

This is my own experience, someone may have better suggestions. First, you can look on the internet for .py .c++ or java matix manupulation tools/small programs run in bash shells. These allow the output from the g:sham or other (2d or 3d) to be turned into mtricies. These can then be fed into

Re: [gmx-users] default -rdd with distance restraints seems too large

Hi Chris, I mentioned that PS would have helped! I am sorry about the confusion. I should have been more clear. I guess you have not followed the particle decomposition threads lately :)) The PD option has been associated some serious issues lately … notably I noticed it does not work well

[gmx-users] genion doesn't recognize SOL in top file

Dear Gromacs users, I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np 8 but it returns a error message saying: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' I checked the

Re: [gmx-users] genion doesn't recognize SOL in top file

On 10/17/13 1:01 PM, sunyeping wrote: Dear Gromacs users, I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np 8 but it returns a error message saying: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section

[gmx-users] KALP in DPPC tutorial reg

Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I have few questions. Please help me to solve it. 1) After the topol.top file has generated from pdb2gmx is it necessary to add

Re: [gmx-users] KALP in DPPC tutorial reg

On 10/14/13 7:47 AM, Sathya wrote: Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I have few questions. Please help me to solve it. 1) After the topol.top file has

Re: [gmx-users] Centering the system

I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? Thanks a lot. Sincerely, Shima On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/13 8:29 AM, Shima

Re: [gmx-users] Centering the system

On 10/17/13 2:09 PM, Shima Arasteh wrote: I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? trjconv -center or trjconv -fit transxy -Justin --

[gmx-users] OPLS-AA parameters for Phospho-threonine and serine

I've searched the literature and internet and can't seem to find anything. I need to rerun some simulations I've run previously with OPLS-AA (and eventually gromos 54A7 when I'm done with OPLS) and need to include phosphorylated residues. I'm parameterized residues in Amber and Charmm, so I'm

Re: [gmx-users] OPLS-AA parameters for Phospho-threonine and serine

Hi, Have look here: http://haddock.science.uu.nl/services/HADDOCK/library.html The ff used by HADDOCK is oplsx derived from opls. Maybe you can exploit them as starting point. Hope it helps And Martin, Erik W erik.mar...@stjude.org ha scritto: I've searched the literature and internet and

[gmx-users] Problem with reading AMBER trajectories

Dear Gromacs users, I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few analysis. Unfortunately I ended-up with the following error. GROMACS will now assume it to be a trajectory and will try to open it using

[gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

(Redirected from gmx-developers) The only way I can reproduce those symptoms is if I delete (or otherwise make unreadable) various parts of src/gmxlib. You may have deleted some files or been a different user at some point. I suggest you do a fresh unpack of the tarball and try again. Mark On

[gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

Thank you, Mark! It was already tried. I mean a fresh unpacking and further cmake run. As for your first thought concerning a loss of access to some parts of gmxlib: [alemasov@nks-g6 gromacs-4.6.3]$ ls -l ./src/gmxlib/ | grep -e - | cut -d' ' -f 1 | sort -n | uniq drwxr-x--- -rw-r-

Re: [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov suc...@gmail.com wrote: Thank you, Mark! It was already tried. I mean a fresh unpacking and further cmake run. As for your first thought concerning a loss of access to some parts of gmxlib: [alemasov@nks-g6 gromacs-4.6.3]$ ls -l

[gmx-users] Centering the system

Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of

Re: [gmx-users] Centering the system

On 10/16/13 8:29 AM, Shima Arasteh wrote: Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups.

Re: [gmx-users] Centering the system

Hi. You should use the following command to center your protein: trjconv -f trajectory.xtc -o corrected_trajectory.xtc -pbc mol -center -s trajectory.tpr Don't forget to replace trajectory with corresponding filenames 2013/10/16 Shima Arasteh shima_arasteh2...@yahoo.com Dear gmx users, I

[gmx-users] Re: gro file formate error

Please keep all Gromacs-related correspondence on the gmx-users mailing list. I am CC'ing this reply to the list and ask that all future discussion occur there. On 10/16/13 9:47 AM, sunyeping wrote: Dear Dr. Lemkul, I am working with protein-ligand system and I have prepared the gro file of

[gmx-users] Constraint bonds and contribution to pressure

Dear all I am simulating simple bead-rod polymer chains, so I apply constraints to all the bonds of my system using the p-lincs algorithm. I try to understand how do the constraint forces contribute to the pressure of the system, but I am a bit confused. Can anyone help? Regards, Tommy --

[gmx-users] KALP-15 in DPPC tutorial

Hi, I am new gromacs user. Now I am learning gromacs using KALP-15 in DPPC tutorial. Before Equilibration the following command is used. make_ndx -f em.gro -o index.ndx In the tutorial it has been described to Merge the Protein and DPPC groups by entering 1 | 13 at

Re: [gmx-users] KALP-15 in DPPC tutorial

On 10/16/13 11:29 AM, Sathya wrote: Hi, I am new gromacs user. Now I am learning gromacs using KALP-15 in DPPC tutorial. Before Equilibration the following command is used. make_ndx -f em.gro -o index.ndx In the tutorial it has been described to Merge the

[gmx-users] Is the website of Martini Force Field down for maintenance?

Dear GMX users, I am going to do some coarse-grained simulations in which the lipid bilayeris covered by polysarccharide. I remember the website of Martini Force Field (http://md .chem.rug.nl/cgmartini/) provides a database for sugar including .itp and . gro files of long chains of different

Re: [gmx-users] Is the website of Martini Force Field down for maintenance?

On 10/16/13 4:29 PM, 朱文鹏 wrote: Dear GMX users, I am going to do some coarse-grained simulations in which the lipid bilayeris covered by polysarccharide. I remember the website of Martini Force Field (http://md .chem.rug.nl/cgmartini/) provides a database for sugar including .itp and . gro

[gmx-users] Gibbs Energy Calculation and charges

We have a molecule, and have run two sets of Gibbs energy calculation, making the charge disappear. One molecule has the normal charges, the other all the charges are doubled. Taking the dHdl results for both and plotting against the charge of a selected atom (charge based at each lambda

[gmx-users] RE: Gibbs Energy Calculation and charges

Here is the molecule in octanol http://ozreef.org/stuff/octanol.gif And here in water http://ozreef.org/stuff/water.gif Just realised, it is actually quite different in water, consistently. So the only difference between the two simulations is the charges on the molecule have been multiplied

[gmx-users] Gibbs Energy Calculation and charges

Dear Dallas: Am I correct that you are saying that for both the regular-charge and double-charge solute molecule, you decoupled the solvent-solute charge-charge interactions and expected that the dH/dL and overall free energy values of the double-charge solute would be exactly two times the

[gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition

[gmx-users] MD of lipid bilayer

Dear Justin, I am currently working on Dynamics study of DPPC lipid bilayer and chromium ions.. I want to know how to insert chromium ions into lipid bilayer. Is there any software for this? Please suggest some idea about how to insert chromium ions into DPPC. When i

Re: [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

Hello, Mark! 16.10.2013 18:17, Mark Abraham wrote: On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov suc...@gmail.com wrote: Thank you, Mark! It was already tried. I mean a fresh unpacking and further cmake run. As for your first thought concerning a loss of access to some parts of

[gmx-users] RE: Gibbs Energy Calculation and charges

Chris, You are correct in the first part of your statement, part that isn't correct is I expect for the same charge on the atom I expect it to give the same dH/dl value. For example, for the OE atom that I provided the graphs for ( http://ozreef.org/stuff/octanol.gif and

[gmx-users] Gibbs Energy Calculation and charges

Ah, I see. I guess that you are using couple-intramol = no (the default in v4.6.3 at least). That means that the intramolecular charge-charge interactions are always at full-strength (and therefore different). I would expect that normal at lambda=0 should be the same as double at lambda=0.5

[gmx-users] default -rdd with distance restraints seems too large

I have a system that also uses a set of distance restraints The box size is: 7.12792 7.12792 10.25212 When running mdrun -nt 8, I get: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 3.62419 nm However, the

Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

Assuming you're using LINCS, from the manual: With domain decomposition, the cell size is limited by the distance spanned by *lincs-order*+1 constraints. Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance for 5 bonds. Which means that you're probably using too many nodes for

Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

Thanks for you reply. I am doing simulation for ionic liquids BMIM + CL. Total number of atoms are 3328. Nilesh Assuming you're using LINCS, from the manual: With domain decomposition, the cell size is limited by the distance spanned by *lincs-order*+1 constraints. Assuming a default

[gmx-users] RE: Gibbs Energy Calculation and charges

Chris, Thank you, that appears to be the issue then. Running them again now with couple-intramol = yes Will report back once that is completed with the results. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University

Re: [gmx-users] recalculating .trr from .xtc

Interactions will be off, especially the bonded terms. On Oct 15, 2013, at 7:21, Mark Abraham mark.j.abra...@gmail.com wrote: Also, the precision was selected when the xtc file was written, ie in the mdp file. Mark On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] Number of ligand contacts over the trajectories

Thanks a lot for reply. On Mon, Oct 14, 2013 at 12:34 PM, bipin singh bipinel...@gmail.com wrote: g_mindist with -on and -d option. On Mon, Oct 14, 2013 at 11:37 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am working with protein-ligand interaction. I would like

Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

On Thu, Oct 10, 2013 at 2:34 PM, James jamesresearch...@gmail.com wrote: Dear Mark, Thanks again for your response. Many of the regression tests seem to have passed: All 16 simple tests PASSED All 19 complex tests PASSED All 142 kernel tests PASSED All 9 freeenergy tests PASSED All 0

[gmx-users] topology file of ligand

Dear gromacs users,   I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he  immediately notice three things that are wrong with this topology, which include

Re: [gmx-users] topology file of ligand

On 10/15/13 11:24 AM, sunyeping wrote: Dear gromacs users, I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that

答复: [gmx-users] topology file of ligand

Thank you Dr. Lemkul,   Could you recommand some primary literatures which are most usefule for me to understand the force field?  Yeping Sun Institute of Microbiology, Chinese Academy of Sciences --发件人：Justin Lemkul

Re: 答复: [gmx-users] topology file of ligand

On 10/15/13 12:25 PM, sunyeping wrote: Thank you Dr. Lemkul, Could you recommand some primary literatures which are most usefule for me to understand the force field? The ones cited in the Gromacs manual are a good start. One should never attempt to use a force field without

[gmx-users] Number of ligand contacts over the trajectories

Dear Gromacs users, I am working with protein-ligand interaction. I would like to calculate the number of contacts ligand make with the protein within a specific cut off ( say within 3.5 to 4.5 angstroms), along the simulation trajectories. Is there any Gromacs analysis script, which can help me

Re: [gmx-users] Number of ligand contacts over the trajectories

g_mindist with -on and -d option. On Mon, Oct 14, 2013 at 11:37 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am working with protein-ligand interaction. I would like to calculate the number of contacts ligand make with the protein within a specific cut off ( say within

[gmx-users] KALP in DPPC tutorial reg

Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html After generating the new position restrain file, I start to energy minimization to get the correct area per lipid. As below:

[gmx-users] Re: Steered MD

First of all, sorry for the late answer. More generally it is said the the rupture force depends logarithmically on the loading rate (velocity times spring constant). - So the rup.force should also depend logarithmically on the spring constant (in the simple bell modell). Think the reason,

Re: [gmx-users] DSSP problem

On 10/13/13 11:56 PM, Mass wrote: Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l -rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr Try giving readable permissions to all, i.e. chmod +r.

Re: [gmx-users] KALP in DPPC tutorial reg

On 10/14/13 2:44 AM, Sathya wrote: Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html After generating the new position restrain file, I start to energy minimization to get

[gmx-users] g_sham

Dear all gromacs users I am creating free energy landscape using g_sham but my axis are not getting labelled. I have searched the archive and found that using xmin and xmax options we can label them. I have first created my 2D projection xvg file using g_anaeig -f *.xtc -s *.tpr -first 1 -last 2

Re: [gmx-users] g_sham

On 10/14/13 7:54 AM, pratibha kapoor wrote: Dear all gromacs users I am creating free energy landscape using g_sham but my axis are not getting labelled. I have searched the archive and found that using xmin and xmax options we can label them. I have first created my 2D projection xvg file

[gmx-users] Wall option with 12-6 LJ

Dear all, I am trying to apply wall options using 12-6 LJ potential. Right now I am using isotropic Berendsen pressure coupling, my first question is, is that the correct method? When I tried to use semi isotropic pressure coupling, the box dramatically expanded. And below is the simulation

[gmx-users] problem in NPT equilibration step

Dear Gromacs user, I am trying to simulate a protein (nmr structure).I have successfully done energy minimisation step.Also I have equilibrated the system a 298 k (which is achieved from 100 ps run) .Now,I am trying to equilibrate the system at 1 bar pressure.After a run of 100 ps ,I am getting

Re: [gmx-users] problem in NPT equilibration step

Hi, Parrinello-Rahman coupling usually allows wide fluctuations in the pressure. I would suggest to take Berendsen algorithm for equilibrating your system, and then extend the simulation with PR if you need to. Bests, baptiste 2013/10/14 Preeti Choudhary preetichoudhary18111...@gmail.com

Re: [gmx-users] problem in NPT equilibration step

The barostat tries to equilibrate the system at the desired pressure, there will be fluctuations and these fluctuations are little higher for Parrinello-rahman if started far away from equilibrium value. I would suggest to start from berendsen and then extend it to P-R. Also, you should run little

Re: [gmx-users] problem in NPT equilibration step

http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and http://www.gromacs.org/Documentation/Terminology/Pressure are useful here. Mark On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary srinathchowd...@gmail.comwrote: The barostat tries to equilibrate the system at the desired

[gmx-users] LJ - SR and Coulbom - SR mdp options

Dear Gmx Users, I want to obtain average Protein-Ligand SR electrostatics and LJ energy values using g_energy from NPT equlibration with position restraints. I used energygrps = Protein LIG However, when I run g_energy -f npt.edr -s npt.tpr I see neither Protein-LIG for any of them. Would you

Re: [gmx-users] LJ - SR and Coulbom - SR mdp options

On 10/14/13 2:03 PM, Steven Neumann wrote: Dear Gmx Users, I want to obtain average Protein-Ligand SR electrostatics and LJ energy values using g_energy from NPT equlibration with position restraints. I used energygrps = Protein LIG However, when I run g_energy -f npt.edr -s npt.tpr I see

Re: [gmx-users] recalculating .trr from .xtc

On 10/14/13 7:56 PM, Leandro Bortot wrote: Dear GROMACS users, Does anyone know how significant is the difference between the original .trr file from a simulation and a recalculated .trr from a whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)? I mean... do you know how big

Re: [gmx-users] recalculating .trr from .xtc

Also, the precision was selected when the xtc file was written, ie in the mdp file. Mark On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/13 7:56 PM, Leandro Bortot wrote: Dear GROMACS users, Does anyone know how significant is the difference between the

Re: [gmx-users] energy drift - comparison of double and single precision

On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: 2013/10/12 Mark Abraham mark.j.abra...@gmail.com Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than

[gmx-users] Gromacs on Stampede

Why not put it in a slurm script and submit that script as a (probably single-node) job. It is not generally acceptable to use a large fraction of the head node of a shared resource for a substantial amount of time. If your problem is different and of a gromacs nature, you may need to

Re: [gmx-users] DSSP problem

Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l total 92332632 -rw-rw-r-- 1 Mass Mass 0 Sep 8 19:46 310Helix.dat -rw--- 1 Mass Mass 371878 Aug 21 07:39 3BLG_115XrayWater.top -rw-rw-r-- 1 Mass

Re: [gmx-users] energy drift - comparison of double and single precision

Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in

Re: [gmx-users] energy drift - comparison of double and single precision

2013/10/12 Mark Abraham mark.j.abra...@gmail.com Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are

Re: [gmx-users] energy drift - comparison of double and single precision

2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Thanks for the suggestion. I'll try next week and I'll show the results ASAP. Guillaume Similar flags apply to temperature and pressure and I believe might seriously

[gmx-users] DSSP problem

Dear users; I am trying to run DSSP and have problem, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error,  Program do_dssp, VERSION 4.6.3 Source code file:

Re: [gmx-users] DSSP problem

On 10/12/13 6:08 PM, Mass wrote: Dear users; I am trying to run DSSP and have problem, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code

Re: [gmx-users] Gromacs on Stampede

Hello, I have a question about running gromacs utilities on Stampede and hopefully someone can point me in the right direction. I compiled gromacs using instructions in this thread and mdrun works fine. Also, some utilities like g_energy, g_analyze (single - core utilities, I believe) seem to

[gmx-users] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)

Hello everybody, I am sorry to do this, but I only have knowledge in ochem (haven't taken pchem yet) so reading Car-Parrinello Molecular Dynamics and searching it on wikipedia yields no data that I understand. So what I'll do to save everyone time is to share what I want to do and ask if this

<    2   3   4   5   6   7   8   9   10   11   >