[gmx-users] Re: Fwd: about the pulling

Thanks Justin! On 10/17/11, Justin A. Lemkul jalem...@vt.edu wrote: Tom wrote: Justin you have good experience of pulling. If you have time, please help with this publling problem: abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot! I already commented:

Re: [gmx-users] lost ngmx

On Sat, Oct 29, 2011 at 12:51 AM, Victor nicegrom...@live.cl wrote: Hello gmx-users I have  compiled gromacs on Debian/Linux wiht the option --with-x but the ngmx binary has not been generated. I don´t have gnome or kde installed, but I have installed xserver-xorg and I can export VMD with

[gmx-users] Interfacial tension of liquid-liquid system

Dear all, I am trying to calculate interfacial tension between Xylene/CHCl3 mixture and water. I have created a box (5*5*15) with a water layer in the middle. I run NVT for 200ps to stabilize the temperature (298 K). After that I run NPT equilibration for ref_p =1 bar with Berendsen isotropic

[gmx-users] System heating up during MD run? (Implicit solvent)

I've been having problems getting implicit solvent systems (which are probably fairly experiment still in gromacs) to work correctly. I've been modelling a protein of about 11000 atoms with hydrogens in a 2 ns simulation. By the end of the simulation, the temperature has risen from 300 K to 496

[gmx-users] Re: Dear Chaban lincs warning

Hello Ahmet: The warnings originating from the LINCS algorithm are dee to either incorrect topology (TOP file) of certain particle or bad initial configuration (GRO file). If you don't provide this information about your problematic system, there is no chance to help you. -- Dr. Vitaly V.

[gmx-users] Prosessing of the pre-eqilibrated lipid bilayer

Dear Gromacs Users! I wounder to know about possible algorithm of preparation of the existing lipid bilayer for further simulation. E.g I have some pre-equilibrated bilayer consisted of symmetrical lipid organization. Now I'd like to remove some lipids from the edges of my bilayer to reduce

[gmx-users] how to calculate the force between two groups

Dear Gromacs Users, I have a question about how to ouput the force between two groups. Suppose the system consists of the groups: A, B, C and D. I need the force only between the groups A and B. g_traj looks only to be able to report the overal forces and cann not distiguish the forces from

Re: [gmx-users] problem with Threading during run

On Mon, Oct 31, 2011 at 9:28 AM, Sanku M msank...@yahoo.com wrote: Hi,  I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make use of threading introduced in gromacs 4.5.x series, it does not work.  After issuing command like mdrun -v -s , I expected that for my 8-core

Re: [gmx-users] how to calculate the force between two groups

On 31/10/2011 4:05 AM, Tom wrote: Dear Gromacs Users, I have a question about how to ouput the force between two groups. Suppose the system consists of the groups: A, B, C and D. I need the force only between the groups A and B. g_traj looks only to be able to report the overal forces and

[gmx-users] average structure

Greeting i'm doing a MD simulation for a monomeric protein over 10 ns, my question is : * for my MD how do i know that it has equilibrated and suitable for study ?,is it RMSD , Radius of gyration and potential energy stability enough ? OR should i look for other parameters and do multiple

[gmx-users] position restraints on heavy atoms or all?

Hello all, I am using amber99SB to model an antibody with organic ligands. I know we could choose to restrain all atoms or only heavy atoms during the equilibration. But I wonder if this really matters for my system. As far as I know, equilibration is aimed at getting the temperature and

Re: [gmx-users] Normal Mode Analysis

Mark, hello! I think that there is some error durins saving of my minimization data As the result of the minimization I've obtained (1) Low-Memory BFGS Minimizer converged to machine precision in 3723 steps, but did not reach the requested Fmax 0. Potential Energy = 2.08789280994511e+03

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

On 24.10.2011 23:23, Szilárd Páll wrote: I've just realized that both you and the similar report you linked to were using CMake 2.8.3. If you don't succeed could you try another CMake version? I could replicate the error with the simple cmake inviocation you proposed in your reply: cmake

Re: [gmx-users] System heating up during MD run? (Implicit solvent)

Hi There has been a number of reports lately about ill-behaving simulations using implicit solvent. I'm currently trying to investigate the cause of this, as such simulations used to work very nice in our hands. In the meantime I would advice to use implicit solvent with caution. Thanks /Per

[gmx-users] Structure preparation for the simulation

Dear Gromacs Users! I'd like to know about external software wich could be used for structure processing for the futher simulation in Gromacs. Today I've tried one of the most popular such software Amber tools but I've forced with problems during compilation of it ) So I'm looking for possible

Re: [gmx-users] Normal Mode Analysis

James Starlight wrote: Mark, hello! I think that there is some error durins saving of my minimization data As the result of the minimization I've obtained (1) Low-Memory BFGS Minimizer converged to machine precision in 3723 steps, but did not reach the requested Fmax 0. Potential Energy =

Re: [gmx-users] System heating up during MD run? (Implicit solvent)

I would also add that the settings provided below probably produce severe cutoff artifacts. In my experience, the only stable settings are those of the all-vs-all kernel (with infinite cutoffs). -Justin Per Larsson wrote: Hi There has been a number of reports lately about ill-behaving

[gmx-users] Nonbonded energy Protein-Ligands

Dear Gmx Users, My system consists of 10 ligands and protein. I am calculating the hydrogen bonds between each residue and my ligands (LIG). The overall charge of each ligand is zero. I used: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num RESIDUEwithLigandsHbond.xvg And I found one residue

Re: [gmx-users] average structure

On 31/10/2011 7:39 PM, larifsofiene wrote: Greeting i'm doing a MD simulation for a monomeric protein over 10 ns, my question is : * for my MD how do i know that it has equilibrated and suitable for study ?,is it RMSD , Radius of gyration and potential energy stability enough ? OR should i

Re: [gmx-users] Nonbonded energy Protein-Ligands

On 31/10/2011 10:19 PM, Steven Neumann wrote: Dear Gmx Users, My system consists of 10 ligands and protein. I am calculating the hydrogen bonds between each residue and my ligands (LIG). The overall charge of each ligand is zero. I used: g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num

Re: [gmx-users] problem with Threading during run

On 31/10/2011 3:36 PM, lina wrote: On Mon, Oct 31, 2011 at 9:28 AM, Sanku Mmsank...@yahoo.com wrote: Hi, I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make use of threading introduced in gromacs 4.5.x series, it does not work. After issuing command like mdrun -v

[gmx-users] Number of nodes

Dear Users, I was trying to run a simulation (gromacs4.5.3) on a Bluegene/L machine. But I was unable to run. System admin say that I need to change the input file. I am not sure what needs to be changed in the input file which specifies no. of nodes usage. I am not familiar with the bluegene

[gmx-users] Re: Dear Chaban lincs warning

ahmet yıldırım: If you want a personal mentoria, you will need to pay for it first. If you strive to get a FREE help, all correspondence should be kept in the mailing list to save up an archive for other gromacs users. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester,

[gmx-users] Re: Dear Chaban lincs warning

You should provide topology file, I do NOT need your MDP files. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA 2011/10/31 ahmet yıldırım ahmedo...@gmail.com: Dear Dr. Chaban, Firstly, thanks for your

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

On 30/10/2011 8:56 AM, Mirco Wahab wrote: On 24.10.2011 23:23, Szilárd Páll wrote: I've just realized that both you and the similar report you linked to were using CMake 2.8.3. If you don't succeed could you try another CMake version? I could replicate the error with the simple cmake

Re: [gmx-users] position restraints on heavy atoms or all?

On 30/10/2011 11:04 AM, Yun Shi wrote: Hello all, I am using amber99SB to model an antibody with organic ligands. I know we could choose to restrain all atoms or only heavy atoms during the equilibration. But I wonder if this really matters for my system. As far as I know, equilibration is

[gmx-users] Re: Structure preparation for the simulation

Dear Gromacs Users! I'd like to know about external software wich could be used for structure processing for the futher simulation in Gromacs. Today I've tried one of the most popular such software Amber tools but I've forced with problems during compilation of it ) So I'm looking for

Re: [gmx-users] Adding Hydrogens by pdb2gmx

James Starlight wrote: Dear Gromacs Users! I could not find how I can add missing hydrogens after their removing by pdb2gmx -ignh. I have modified structure of my protein after editing by some soft and I removed all hydrogens but now I want to add it back in accordance with gromos ff

Re: [gmx-users] Adding Hydrogens by pdb2gmx

Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh with gromos force field I've checked conf.gro by VMD and this structure didnt contains any hydrogens ;o James 2011/10/31 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Dear Gromacs Users! I could not find

Re: [gmx-users] Adding Hydrogens by pdb2gmx

James Starlight wrote: Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh with gromos force field I've checked conf.gro by VMD and this structure didnt contains any hydrogens ;o I highly doubt that. I've used one of the Gromos96 force fields for nearly all of my

Re: [gmx-users] Number of nodes

Hello, System Admin said that the Job fails on 32 and 128 because memory is insufficient for each task, so upon increasing the nodes, data gets distributed across more number of nodes and each node gets less memory occupancy and he also mentioned that he was able to run on 512 nodes but it was

Re: [gmx-users] Number of nodes

On 31/10/2011 11:29 PM, Kavyashree M wrote: Hello, System Admin said that the Job fails on 32 and 128 because memory is insufficient for each task, so upon increasing the nodes, data gets distributed across more number of nodes and each node gets less memory occupancy and he also mentioned that

[gmx-users] Mismatching in Bergers DMPC bilayer lipid topology

Dear James: Next time, please specify exactly what you did in enough detail for somebody else to reproduce it, much as in a manuscript. e.g. there is no dmpc.gro in that website. I can guess what you did, but that is not ideal. I took a look at the files that I suppose you used and the

Re: [gmx-users] Adding Hydrogens by pdb2gmx

exactly all hydrogens were represented as a part of the groupd in wich they were. So is there possible way to explicit it? Another question about pdb2gmx. about -term as I understood this must be used only if atoms for CAP groups are presented in the PDB file mustnt it? So what term exactly do?

Re: [gmx-users] Adding Hydrogens by pdb2gmx

James Starlight wrote: exactly all hydrogens were represented as a part of the groupd in wich they were. So is there possible way to explicit it? I'm not quite sure I follow. A united atom force field, by definition, does not have aliphatic hydrogens. I suggest you consult the

[gmx-users] Re: Prosessing of the pre-eqilibrated lipid bilayer

So does anobody know possible sollution for the reduce size of the existing bilayer? E.g I've preequilibrated 128 lipids in bilayer and want to obtain 32 lipid bilayer and dont perturb overall topology of the system In my lab there is only extremely weak CPU. it could not make md for large systems

Re: [gmx-users] Simulation of membrane protein

In some papers I found Gromacs graphs showed indirectly measurements of the time evolution of the Area per lipid value. What gromac's program could be used for it for cheacking the above value during simulation runs ? JAmes 2011/10/29 James Starlight jmsstarli...@gmail.com It's appeared new

[gmx-users] LINCS crushes

Hi, all! I am trying to simulate a system of peptide, water, NaCl and DMSO. I used pdb2gmx to generate .top file for DMSO and then created this .itp: (initial DMSO structure had been minimized before it was used for box generation) [ moleculetype ] ; Namenrexcl DMSO 3

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: In some papers I found Gromacs graphs showed indirectly measurements of the time evolution of the Area per lipid value. What gromac's program could be used for it for cheacking the above value during simulation runs ? There is no Gromacs tool for this. For a

Re: [gmx-users] LINCS crushes

Yuri Garmay wrote: Hi, all! I am trying to simulate a system of peptide, water, NaCl and DMSO. I used pdb2gmx to generate .top file for DMSO and then created this .itp: (initial DMSO structure had been minimized before it was used for box generation) [ moleculetype ] ; Name

[gmx-users] Re: Re: Re: Reference structure for g_covar

Hi Tsjerk, Thanks for your earlier reply. It makes things clear. Is it possible that the cosine content of first PC is high because of the fluctuations in the long loop regions which dominate and not in the secondary structures. The fluctuations in the loop regions is of no interest to me and

[gmx-users] Jarzinsky's inequality from SMD simulation

Hi,   I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of   extracting PMF from SMD simulations.  If not, can anyone

Re: [gmx-users] Simulation of membrane protein

Thanks, Justin I'll test your program soon. Today also I have some problems with generation of the posre for lipids I have lipid bilayer in pdb. Then I selected one lipid molecule and move it to separate pdb and convert it to gro via editconf. Than I've used genres and generate posre file for 1

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Thanks, Justin I'll test your program soon. Today also I have some problems with generation of the posre for lipids I have lipid bilayer in pdb. Then I selected one lipid molecule and move it to separate pdb and convert it to gro via editconf. Than I've used genres

Re: [gmx-users] Simulation of membrane protein

I've done all of that i have posre_lipid.itp - for 1 lipid ( posres for each of 50 atoms ) I've included this in the topology of the bilayer ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include dppc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ;

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

There is a way to extract the PMF from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html - Laura On 10/31/2011

Re: [gmx-users] Simulation of membrane protein

On 1/11/2011 3:00 AM, James Starlight wrote: I've done all of that i have posre_lipid.itp - for 1 lipid ( posres for each of 50 atoms ) I've included this in the topology of the bilayer ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include dppc.itp ; Include water

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: I've done all of that i have posre_lipid.itp - for 1 lipid ( posres for each of 50 atoms ) I've included this in the topology of the bilayer ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include dppc.itp ; Include water topology #include

Re: [gmx-users] LINCS crushes

Try minimizing again now with all bonds constrained using the output of the EM that ran. Generally, if EM crashes, your system contains some unresolvable clash or inappropriate geometry. Perhaps you have now relaxed the bad interactions sufficiently to proceed. I had examined structure

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

Hi Laura,   I do not think Justin Lemkul's tutorial is suggesting extracting PMF using SMD simulation. What is does that it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. On 10/31/2011 01:29 PM, Sanku M wrote: using SMD simulation. What is does that

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

Laura Kingsley wrote: Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. One approach:

[gmx-users] Re: how to calculate the force between two groups (Mark Abraham)

Thanks Mark! It was actually what I did. mdrun -rerun with well-chosen energy group exclusions only gives the energy between certain pairs of group, not the forces. g_traj gives the overall forces not the force between certain pair. Thanks a lot for any further idea to obtain the force for

[gmx-users] gromacs query

I m using gromacs 4.5.3 version and trying to simulate a protein in liquid media but I found problem in eqilibration step especially when I give following command: mdrun -deffnm nvt .After giving this command it is showing error,i.e., There is no domain decomposition for 4 nodes that is

Re: [gmx-users] gromacs query

Anushree Tripathi wrote: I m using gromacs 4.5.3 version and trying to simulate a protein in liquid media but I found problem in eqilibration step especially when I give following command: mdrun -deffnm nvt .After giving this command it is showing error,i.e., There is no domain

Re: [gmx-users] Re: Structure preparation for the simulation

Hi James, I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html). Despite being an old and not well supported for any system, it is still a free and easy to use and allows the building and mutating of residues in addition to automatically adding missing atoms. You can just

[gmx-users] equilbium convergence and RMSD structure

Greeting I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated forms has converged to equilibrium and simulation is suitable for analysis. The 4 MD simulations are done in cubic water volume, 500 ps of steepest descent minimization , with 100 ps of NVT ensemble and 100 ps of NPT

Re: [gmx-users] equilbium convergence and RMSD structure

larif sofiene wrote: Greeting I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated forms has converged to equilibrium and simulation is suitable for analysis. The 4 MD simulations are done in cubic water volume, 500 ps of steepest descent minimization , with 100 ps of NVT

[gmx-users] Re: how to calculate the force between two groups (Mark Abraham)

On 1/11/2011 5:40 AM, Tom wrote: Thanks Mark! It was actually what I did. mdrun -rerun with well-chosen energy group exclusions only gives the energy between certain pairs of group, not the forces. Did you use nstfout to actually write the forces? g_traj gives the overall forces not the

Re: [gmx-users] LINCS crushes

On 1/11/2011 3:43 AM, Yuri Garmay wrote: Try minimizing again now with all bonds constrained using the output of the EM that ran. Generally, if EM crashes, your system contains some unresolvable clash or inappropriate geometry. Perhaps you have now relaxed the bad

[gmx-users] unknown cmap torsion between atoms

Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381

Re: [gmx-users] unknown cmap torsion between atoms

Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot show any error. Cant the charmm gui built

Re: [gmx-users] unknown cmap torsion between atoms

On 1/11/2011 2:16 PM, ram bio wrote: Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot

[gmx-users] xtc vs. trr file

Dear all, I am low on disk space and need to delete trr files. I turned on -x option in all runs so generated xtc files as well. Just wondering if xtc files contain less information than trr ones which make xtc have less size. Am I going to lose any information other than velocities? Thanks, J.

Re: [gmx-users] xtc vs. trr file

On 1/11/2011 3:30 PM, Juliette N. wrote: Dear all, I am low on disk space and need to delete trr files. I turned on -x option in all runs so generated xtc files as well. Just wondering if xtc files contain less information than trr ones which make xtc have less size. Am I going to lose any