RE: [gmx-users] g_energy

Hello, I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen. Could you please clarify how it is calculated? In a system with a protein and water, what does it correspond to? Best, Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...

[gmx-users] Editing of the existing system

Dear Gromacs Users! I have some system wich consist of protein in membrane-mimicking layer surrounded by water. I want to modify my existing system by adding small peptide fragment to this system. I want to dock this peptide to the some part of my protein wich is situated in the bottom water lay

Re: [gmx-users] protein melting experiment by GROMACS

Acoot Brett wrote: Dear All, I remember before I have read a something on melting the protein from a predefined starting temperature to a predefined end temperature by MD, so that after the MD we can look at the whole process to see which part of the protein unfold earlier, which part of t

Re: [gmx-users] protein melting experiment by GROMACS

On 30/03/2012 12:11 PM, Acoot Brett wrote: Dear All, I remember before I have read a something on melting the protein from a predefined starting temperature to a predefined end temperature by MD, so that after the MD we can look at the whole process to see which part of the protein unfold earl

[gmx-users] protein melting experiment by GROMACS

Dear All,   I remember before I have read a something on melting the protein from a predefined starting temperature to a predefined end temperature by MD, so that after the MD we can look at the whole process to see which part of the protein unfold earlier, which part of the protein of the prote

Re: [gmx-users] Not able to continue with Equilibration

On 30/03/2012 8:39 AM, francesca vitalini wrote: Thank you Justin for your answer. I'm trying to add the position restraints to my protein, but I have a problem. My topology is made of a chain repeated twice and if I want to build the position restraints through genrestr from a gro file, the nume

Re: [gmx-users] About the function of "-v' in mdrun

It's almost always a good idea to run with -v because it will output basic state information and time-to-completion estimates as your simulation runs. It prints to "standard out" so if launching mdrun from a script (like on a cluster), make sure the script captures the output to a file. I find

RE: [gmx-users] About the function of "-v' in mdrun

Slang for “it says a lot”, being verbose (which is what –v means), lots of information printed out. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9

[gmx-users] About the function of "-v' in mdrun

Dear All, There is a tutorial says the function of "-v" in mdrun is to make the md process visible in the screen, which is correct. However from the introduction of mdrun in the new version of gromacs, it says the function of "-v" is to make "noisy and loud". Will you please tell me what is th

Re: [gmx-users] How to read in mdcrd files to gromacs?

Dear Cat, > Dear experts, > > I am trying to do the following command: > > /usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v > If you are using -o & -v options you should specify files for them > But the following error message is found: > >

[gmx-users] Re: how to optimize hydrogen bonds before simulation?

> > Hello: > >   I am wondering is it possible to optimize hydrogen bonds network > before simulation? I've got some crystal solvent in the system and I > would like to optimize the hbond network even before building a solvent > system. If you freeze all atoms which are not involved in H-bonds, th

Re: [gmx-users] Not able to continue with Equilibration

Thank you Justin for your answer. I'm trying to add the position restraints to my protein, but I have a problem. My topology is made of a chain repeated twice and if I want to build the position restraints through genrestr from a gro file, the numeration of the atoms would put the 2 chains sequenti

Re: [gmx-users] HB lifetime

29 mar 2012 kl. 18.47 skrev Nidhi Katyal: > Dear All > I would like to know the strength of the given bond by calculating the > lifetime of that bond.For the same reason i used: > g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg > and i got: > TypeRate(1/ps) Time(ps)

Re: [gmx-users] System exploding

Lara Bunte wrote: Hello If gromacs gives the warning that the system could explode, what could be the reason for that? http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar M

[gmx-users] System exploding

Hello If gromacs gives the warning that the system could explode, what could be the reason for that? Greetings -- 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

Re: [gmx-users] how to optimize hydrogen bonds before simulation?

Albert wrote: Hello: I am wondering is it possible to optimize hydrogen bonds network before simulation? I've got some crystal solvent in the system and I would like to optimize the hbond network even before building a solvent system. Provided the starting configuration does not requi

[gmx-users] how to optimize hydrogen bonds before simulation?

Hello: I am wondering is it possible to optimize hydrogen bonds network before simulation? I've got some crystal solvent in the system and I would like to optimize the hbond network even before building a solvent system. THX -- gmx-users mailing listgmx-users@gromacs.org http://lists.

Re: [gmx-users] About desired Spacing in Distance.pl script

vidhya sankar wrote: Dear justin Thank you for your at once reply I have successfully use the Distance.pl I got output. .But in Distance.pl script i have not represented the Any Desired spacing (0.3nm) . Should i Represent? .

[gmx-users] About desired Spacing in Distance.pl script

Dear justin Thank you for your at once reply       I have successfully use the Distance.pl I got output. .But in Distance.pl script i have not represented the Any  Desired spacing (0.3nm) . Should i Represent? . If  i need to represent

[gmx-users] How to read in mdcrd files to gromacs?

Dear experts, I am trying to do the following command: /usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v But the following error message is found: ---Program g_covar_d, VERSION 4.5.5Source code file: trxio.c, line: 870 Fatal error

[gmx-users] Can GROMACS read binpos trajectory files?

Dear Sir, I am using g_covar version 4.0.7. I am trying to do: /share1/gromacs/bin/g_covar -s ../average.pdb -f ../md0.binpos -o -v However, an error message appear: Program g_covar, VERSION 4.0.7Source code file: gmxfio.c, line: 737 Can not open file:../md0.mdcrd.xtc What should I do next? Best

Re: [gmx-users] Velocity autocorrelation

You probably need to save velocities at least every 10 fs; look at your plot on a fine enough time scale - say 0-1 ps range probably running in NVE ensemble would help as well Krzysztof Kuczera On 3/29/12 10:42 AM, Ignacio Fernández Galván wrote: Dear all, I'm trying to estimate the correlatio

[gmx-users] Pressure coupling and Isothermal compressibility for a biphasic system

Hello All, I have some doubts regarding the use of pressure coupling and isothermal compressibility for a biphasic system (octane+water boxes built over each other). I have two questions regarding that: (1) Which pressure coupling (pcoupl) type would be suitable for this type of system ? (2) As

[gmx-users] HB lifetime

Dear All I would like to know the strength of the given bond by calculating the lifetime of that bond.For the same reason i used: g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg and i got: TypeRate(1/ps) Time(ps) ... Forward-0.182-5.495 ... HB lifetime

Re: [gmx-users] About Distance.pl script

Dariush Mohammadyani wrote: I have gotten this error previously. I changed the address of the g_dist (e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works. Yes, the script assumes the command g_dist exists in your $PATH and is unmodified (no prefixes or s

Re: [gmx-users] About Distance.pl script

I have gotten this error previously. I changed the address of the g_dist (e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works. Dariush On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar wrote: > Dear justin , Thank you for your previous reply > When i Download and run Distance.pl scri

Re: [gmx-users] About Distance.pl script

vidhya sankar wrote: Dear justin , Thank you for your previous reply When i Download and run Distance.pl script In your website I got the following error readline() on closed filehandle IN at ./Distance.pl line 16. Use of uninitialized value $distance in concatenation (.) or string at ./D

Re: [gmx-users] Velocity autocorrelation

On 30/03/2012 2:42 AM, Ignacio Fernández Galván wrote: Dear all, I'm trying to estimate the correlation time for my system, for the purpose of selecting a number of uncorrelated configurations and setting a good value for nstxout. My systems are usually small molecules in molecular liquids (w

Re: [gmx-users] about g_mindist....

On 30/03/2012 12:40 AM, rama david wrote: Hi mark .. thank you for your suggestion.. My command line is g_mindist -f ..xtc -s ..tpr -od minimal.xvg -pi protein group contain information about the 284 atom (i.e. All protein atoms) So clearly some part of some molecule is protruding across

[gmx-users] About Distance.pl script

Dear justin , Thank you for your previous reply When i Download and  run Distance.pl script In your website I got the following error readline() on closed filehandle IN at ./Distance.pl line 16. Use of uninitialized value $distance in concatenation (.) or string at ./Distance.pl line 30. How t

[gmx-users] Velocity autocorrelation

Dear all, I'm trying to estimate the correlation time for my system, for the purpose of selecting a number of uncorrelated configurations and setting a good value for nstxout. My systems are usually small molecules in molecular liquids (water, methanol, acetonitrile, cyclohexane...). As a firs

Re: [gmx-users] Not able to continue with Equilibration

francesca vitalini wrote: My minimization was done without any constraints. I'm starting using constraints only in the nvt equilibration as I'm trying to equilibrate my solvent, so, maybe here I'm being extremely naïve, but, shouldn't I avoid fixing the water in the nvt, as equilibrating it is

Re: [gmx-users] Umbrella sampling along Radius of gyration

Hey Chris, It is actually not necessary to go to the code. You can do that by compiling a version of gromacs including the plumed path for free energy calculations. Amogst the several collective variables included there there is gyration radius. Regards Felipe Mensaje original---

Re: [gmx-users] Not able to continue with Equilibration

My minimization was done without any constraints. I'm starting using constraints only in the nvt equilibration as I'm trying to equilibrate my solvent, so, maybe here I'm being extremely naïve, but, shouldn't I avoid fixing the water in the nvt, as equilibrating it is exactly the reason I'm running

Re: [gmx-users] Not able to continue with Equilibration

francesca vitalini wrote: Hallo Felix, thank you for your answer. I tried the constraints = h-bonds but no change in the output. If I look at the step.pdb file that is produced after the running I have some strange outcome. For example some of my atoms are not recognized as part of my protein a

[gmx-users] Not able to continue with Equilibration

I didn't follow this whole thread, but I sometimes need to turn off all constraints when doing minimization. In fact, for that reason I entirely stopped ever using restraints during energy minimization. In extreem cases, I have had success also by forcing the water to be flexible with a -DF

Re: [gmx-users] Not able to continue with Equilibration

Hallo Felix, thank you for your answer. I tried the constraints = h-bonds but no change in the output. If I look at the step.pdb file that is produced after the running I have some strange outcome. For example some of my atoms are not recognized as part of my protein any more and my structure is de

[gmx-users] Umbrella sampling along Radius of gyration

It is not clear to me how one would do this with MD. The only thing that I can think of doing in gromacs is to create a virtual particle that is placed at the center of the protein and then apply forces along the vector from this virtual atom to each of the Ca atoms. You would need to modif

AW: [gmx-users] Not able to continue with Equilibration

Hello again, Well, I once had problems with simulations crashing randomly during production runs (sometimes after tens of nanoseconds) with the LINCS warnings you described. Switching LINCS from "all-bonds" to only "h-bonds" did the trick for me, although I never exactly figured out why. Maybe

Re: [gmx-users] How to fix Water during simulation ?

ajani haresh wrote: Hello Everyone, I am new in Gromacs. I am using gromacs for protein-ligand complex. I have few question ? 1): how to fix water during simulation ? If pdb2gmx wrote the topology, you should be able to invoke "define = -DPOSRES_WATER" in the .mdp file. Check your topo

Re: [gmx-users] About cutt-off scheme ..

rama david wrote: Hi justin, thank you for reply, 1.I sort out the specific time pdb .. I notice the folllowing things.. 26 and 111 are the atoms of two different protein .. one is on the right hand side near the box boundary ..and other is protruding from the

[gmx-users] How to fix Water during simulation ?

Hello Everyone, I am new in Gromacs. I am using gromacs for protein-ligand complex. I have few question ? 1): how to fix water during simulation ? 2): how to fix protein and ligand during simulation ? 3) how to fix few crystal water molecule during simulation ? 4) how to fix specific water

Re: [gmx-users] About cutt-off scheme ..

Hi justin, thank you for reply, 1.I sort out the specific time pdb .. I notice the folllowing things.. 26 and 111 are the atoms of two different protein .. one is on the right hand side near the box boundary ..and other is protruding from the left hand side box

Re: [gmx-users] About cutt-off scheme ..

rama david wrote: Hi Gromacs friends, Thank you justin for your explaination .. It is, however, common to compromise in this respect, and make the solvent layer somewhat smaller in order to reduce the computational cost. For efficiency reasons the cut-off with triclinic boxes is more restr

Re: [gmx-users] about g_mindist....

Hi mark .. thank you for your suggestion.. My command line is g_mindist -f ..xtc -s ..tpr -od minimal.xvg -pi protein group contain information about the 284 atom (i.e. All protein atoms) .. So please suggest me the right way .. On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham wrote: > On 29/0

Re: [gmx-users] About cutt-off scheme ..

Hi Gromacs friends, Thank you justin for your explaination .. It is, however, common to compromise in this respect, and make the solvent layer somewhat smaller in order to reduce the computational cost. For efficiency reasons the cut-off with triclinic boxes is more restricted. For grid search t

Re: [gmx-users] Not able to continue with Equilibration

Hi! I'm having a similar problem. I have a dimer solvated in a big box of water plus ions that I have managed to minimize correctly (see output of minimization at the end) but when I try to run NVT equilibration (see later) I get LINCS warnings(see below) refearred to atoms which are not in a clust

Re: [gmx-users] Not able to continue with Equilibration

On 29/03/2012 8:22 PM, Hendry wrote: Hi, I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equili

Re: [gmx-users] mpirun

On 29/03/2012 8:09 PM, cuong nguyen wrote: Dear Gromacs Users, as in the manual, I tried to run the simulation on 4 processors and used the command as follow: /mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x NVT_50ns -e NVT_50ns -g NVT_50ns -v/ Then I got the error: /mpirun

Re: [gmx-users] About cutt-off scheme ..

rama david wrote: Hi Gromacs users , as per the link given on gromacs website... Introduction to Molecular Dynamics Simulations and Analysis - Tutorial for performing and analyzing simulations of proteins. Includes examples of many of the grom

[gmx-users] deformations aplying an electric field

Hi, I am trying to simulate a nanotube inserted into a lipid bilayer using Gromacs 4, applying an external electric field (in the direction of the z axis). I have added this line to my input file: ;Electric field E_z = 1 1.0 0 The calculations finish without problem, however I can

[gmx-users] About cutt-off scheme ..

Hi Gromacs users , as per the link given on gromacs website... Introduction to Molecular Dynamics Simulations and Analysis- Tutorial for performing and analyzing simulations of proteins. Includes examples of many of the gromacs analysis tools and addr

Re: [gmx-users] Not able to continue with Equilibration

Dear Felix, Thanks for suggestions. I will try it now. On Thu, Mar 29, 2012 at 5:40 PM, Rausch, Felix wrote: > Hello, > > ** ** > > The results of the energy minimization look reasonable. Nevertheless, you > should (visually) check your equilibration starting structure for problems > (e.

AW: [gmx-users] Not able to continue with Equilibration

Hello, The results of the energy minimization look reasonable. Nevertheless, you should (visually) check your equilibration starting structure for problems (e.g. clashes that could not be solved by EM). It would be a good idea to concentrate on the atom numbers given in the error messages. To

Re: [gmx-users] mpirun

Where did you install your Gromacs? Most likely the executables are not in the PATH. On Thu, Mar 29, 2012 at 5:09 PM, cuong nguyen wrote: > Dear Gromacs Users, > > as in the manual, I tried to run the simulation on 4 processors and used > the command as follow: > *mpirun -np 4 mdrun_mpi -s NVT_5

[gmx-users] Not able to continue with Equilibration

Hi, I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equilibration step below. I have also provided

[gmx-users] mpirun

Dear Gromacs Users, as in the manual, I tried to run the simulation on 4 processors and used the command as follow: *mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x NVT_50ns -e NVT_50ns -g NVT_50ns -v* Then I got the error: *mpirun was unable to launch the specified application

Re: [gmx-users] Calculate Bulk Pressure Tensor?

29 mar 2012 kl. 04.10 skrev Weilong Zhao: > Hi, > > I was trying to calculate the pressure tensors for one of my solid crystal > systems. I notice that g_energy does have this option---pressure xx, pressure > yy and pressure zz, however the results seem to be a function of running > time. How

Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

Thanks Rama, I will do the instructions and do my best.   Cheers, Shima From: rama david To: Discussion list for GROMACS users Sent: Thursday, March 29, 2012 12:57 PM Subject: Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs Hi shima    

Re: [gmx-users] about g_mindist....

On 29/03/2012 7:20 PM, rama david wrote: Hi everybody , I run simulation of 4 same molecule keep apart in box of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 284 ) force field = gromacs96 53a6 COM (center of mass) infirmation of molecules system size :

Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

Hi shima Read the insttruction carefully .. DELETE ALL THE LINE AND SUBSEQUENT LINES IN THE SECTION Delete all the bellow line in that section... It will surely solve your problem (As I also Face the same one ) with best wishes, On Thu, Mar 29, 2012 at 11:23 AM, ros...@kth.se

[gmx-users] about g_mindist....

Hi everybody , I run simulation of 4 same molecule keep apart in box of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 284 ) force field = gromacs96 53a6 COM (center of mass) infirmation of molecules system size : 1.255 1.577 1.883 box vectors : 4.000 4

RE: [gmx-users] Shima Arasteh wants to share a link | Gromacs

Check your topology file. The atom LC3 is not found in Gromacs .atp file. How did you generate your .top file? If you generate it using pdb2gmx it should not give you such error. Cheers, = Emmanuel Birru PhD Candidate Faculty of P

Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

On 29/03/2012 4:53 PM, ros...@kth.se wrote: Shima Arasteh wants to a share a link on the Gromacs wiki: http://www.gromacs.org/ Shima Arasteh says: Dear Gromacs friends, I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction but I face a fatal error when I enter this com

Re: [gmx-users] Pressure coupling doubt

On 29/03/2012 5:38 PM, bipin singh wrote: Hello, I have two doubts regarding pressure coupling in Gromacs: 1) When I use pcoupl=no the mdp.out shows the following ; Pressure coupling pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 ; Time consta

Re: [gmx-users] About movie in GROMACS

On 29/03/2012 4:15 PM, rama david wrote: HI Gromacs Friends, I complete one simulation for 4 different molecule placed apart in box of dimension 4 4 4 .. when I used the trajectory I saw the one molecule interact with each other but they are getting broken because of box..(Some

AW: [gmx-users] About movie in GROMACS

>From my limited experience, ...Also, VMD makes this easier. I learned the hard way to center on a molecule when making the initial box in editconf. Otherwise varied combinations of the -mol, -pbc , -nojump -center options usually work, but never consitent at least for me. Still, if its 4 s