[gmx-users] Instantaneous dipole moment of water molecule

Dear All I want to calculate instantaneous dipole moment of a water molecule(from liquid water) in gromacs.I had gone through the archives of the forum but couldn't found much. I used command g_dipoles with following extension g_dipoles -f 293.trr -s 293.tpr -n atoms.ndx -o Mtot.xvg -mu -1

Re: [gmx-users] strange continued jobs

HI Justin: thanks for such kind comments. I restart the job and it works fine now. best Albert On 09/11/2012 12:50 PM, Justin Lemkul wrote: On 9/11/12 3:11 AM, Albert wrote: hello: I've restart my jobs with command: mpiexec -n 160 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v

[gmx-users] dihedraltypes amber forcefield

Hi everybody, I get the error that something is wrong with the dihedraltype of 4 atoms in my protein when I use the grompp command. I looked at the topology file which atoms are involved in this dehedraltype. Those are the four atoms: CA CA C OS Where can I find out the parameter for this

[gmx-users] Orientation of protein

Dear users, As a matter of fact I don't know the exact orientation of my protein. To insert a protein in a lipid bilayer, I need to set the orientation of protein and bilayer parallel to z-axis. I'd like to know if it is necessary for protein to be in z-direction exactly? Is it acceptable to

Re: [gmx-users] No molecules were defined in the system/ No such molecule type Dio

On 9/12/12 1:58 AM, sarah k wrote: Dear all, I'm trying to simulate several drug-protein complexes on a clustered server. I used PRODRG and editted my .top, .pdb, .gro and posre.itp files. Here is the final lines of my .top file: ; Include Position restraint file ; Include Position

Re: [gmx-users] dihedraltypes amber forcefield

On 9/12/12 3:29 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I get the error that something is wrong with the dihedraltype of 4 atoms in my protein when I use the grompp command. I looked at the topology file which atoms are involved in this dehedraltype. Those are

Re: [gmx-users] Orientation of protein

On 9/12/12 4:28 AM, Shima Arasteh wrote: Dear users, As a matter of fact I don't know the exact orientation of my protein. To insert a protein in a lipid bilayer, I need to set the orientation of protein and bilayer parallel to z-axis. I'd like to know if it is necessary for protein to be

[gmx-users] LINCS warning in md run

Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example: Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous,

[gmx-users] Published articles which have used Gromcas for their work

Dear All Actually I am very interested to know the list of works which have used Gromacs for their work. I searched in both google scholar and scopus, but the results are not the same! of course I looked for all articles that have cited principal papers in Gromacs in:

Re: [gmx-users] LINCS warning in md run

On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example: Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979)

[gmx-users] Re: freeze value

On 9/12/12 4:52 AM, samira ansari wrote: Dear justin, I have a problem with freezing group. I got no answer from gmx_users. I don't recall seeing the original post. In any case, please keep any Gromacs-related correspondence on the mailing list; I am not a private help service. I am

[gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Hello, I have been basing some DPPC bilayer simulations off of files from Justin Lemkul's tutorial, including the .itp files and .mdp files. Everything has been working fine except that my area/lipid seems to be too low and my diffusion coefficient seems to be too slow compared to experimental

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

On 9/12/12 10:56 AM, David Ackerman wrote: Hello, I have been basing some DPPC bilayer simulations off of files from Justin Lemkul's tutorial, including the .itp files and .mdp files. Everything has been working fine except that my area/lipid seems to be too low and my diffusion coefficient

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Hi, The experimental range of diffusion coefficients are quite large for DPPC, plus the force field and simulation parameters can have a large impact upon the diffusion speeds seen in the simulations. We have just published a study comparing force fields for simulating DPPC and POPC

[gmx-users] Calculating tertiary structure rotation

Dear all, I would like to measure the rotation angle of helix movement during MD simulation course. Can you tell me how can I measure and make that rotation angle plot ? Thanks. Rajiv-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Hi, Thank you for your response. As to my concern about incorrect areas and diffusion, I am basing it off of other papers that simulate DPPC bilayers. For instance, in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251217/figure/F12/ , they simulate a DPPC bilayer with DiI molecules in

[gmx-users] About Bond breaking and usage of constraints

Dear justin ,     Thank you fro your Reply   I am doing MD for  Cyclic poly Peptide With ARG as N-termina and PRO as C-terminal .  I have run pdb2gmx it is oak.  . I have solvated and added ions successfully But when i Run the Energy

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Hi, While comparing to other simulations can be useful, I would argue that the real test for the combination of force field and simulation parameters is to determine if the simulated membrane properties compare well to the experimentally determined values. As long as they do this, you can

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

On 9/12/12 1:21 PM, David Ackerman wrote: Hi, Thank you for your response. As to my concern about incorrect areas and diffusion, I am basing it off of other papers that simulate DPPC bilayers. For instance, in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251217/figure/F12/ , they

[gmx-users] Re: About Bond breaking and usage of constraints

On 9/12/12 1:34 PM, vidhya sankar wrote: Dear justin , Thank you fro your Reply I am doing MD for Cyclic poly Peptide With ARG as N-termina and PRO as C-terminal . I have run pdb2gmx it is oak. . I have solvated and added ions successfully But

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Hello, Right I guess my biggest concern was diffusion. I did in fact do 12 simulations of DPPC bilayers for 100 ns each, and still got the aforementioned APL and diffusion. When I turn off the dispersion, I get more appropriate APL and MSD values, that match other papers, even when only looking

[gmx-users] Smaller Area Per Lipid for DPPC Bilayer

While dispersion correction is a great idea that helps to reduce the impact of the precise choice of cutoff distance on the results, the Berger parameters (and indeed all other parameters) were not developed with the inclusion of dispersion correction and one could argue that it is thus

[gmx-users] Error regarding topology and coordinate files

Hi I am trying to run a simulation of the self-assembly of a course-grained lipid bilayer using GROMACS. So far, I have made a box of DSPC lipid molecules (7.5 x 7.5 x 7.5, 128 molecules). I have also added water molecules using the genbox command (768 water molecules added), and named the

Re: [gmx-users] Error regarding topology and coordinate files

On 9/12/12 2:38 PM, Bharath K. Srikanth wrote: Hi I am trying to run a simulation of the self-assembly of a course-grained lipid bilayer using GROMACS. So far, I have made a box of DSPC lipid molecules (7.5 x 7.5 x 7.5, 128 molecules). I have also added water molecules using the genbox

Re: [gmx-users] LINCS warning in md run

Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy

Re: [gmx-users] LINCS warning in md run

On 9/12/12 3:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, my mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

Hi Chris, I'm not so sure as to say that all of the parameters for simulating lipid membranes were not developed with a dispersion correction. The Berger parameterisation used a dispersion correction for the pentadecane simulations which were used to parameterise the tails (although as far

Re: [gmx-users] How to create two parallel wall?

There's a built-in wall option. Check section 7.3.20 of the manual. Otherwise, you could just include coordinates and topologies for walls in your simulation. For your second question, g_density with appropriate index groups. On Wed, Sep 12, 2012 at 4:27 PM, Ali Alizadeh

[gmx-users] Re: How to determin the simulation time

在 2012年9月11日星期二，xiaojing gong 写道： Dear all, Typically, we use over 100 ns to simulate the transport progress. But *How the sufficient number of iterations and these times has been determined? Are there some convergence tests ?* * * *Many thanks!* *YLK* * * ** -- gmx-users

[gmx-users] Re: time constant in V-rescale algorithm

在 2012年9月11日星期二，xiaojing gong 写道： Dear all, When use the V-rescale algorithm , how to choose the time constant value, I saw some choose 0, some choose 0.1 ps. Are there some standard for choosing the time constant? Best YLK -- gmx-users mailing list

[gmx-users] Calculating secondary structure movements

Dear all, I would like to measure the rotation angle of helix movement during MD simulation course. Can you tell me how can I measure and make that rotation angle plot ? Thanks. Regards Rajiv -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Resuming of calculation from last *.cpt

Dear Gromacs Users! I'm looking for possible way to resume trajectory calculations after that calculations have been stoped. Typically in such cases I start new task using cpt file from incomplete run. This produce new trajectory which start from the last frame of previous run. After that I