Re: [gmx-users] Position restraining of ions.

You can copy the part regarding the certain ion type from ions.itp to a separate itp file and #include that itp file into a top file. Then #include the position restraint file that has restraints for only one ion of that type at the end of that new itp file. By this manner you can even split a

Re: [gmx-users] Position restraining of ions.

Hi, Thanks for your prompt reply. I have modified the top file as shown below. Though it looks working fine for me, can you please have quick look into it. *** r ; Force field was read

Re: [gmx-users] Problem running equilibration step

Hi, The error is rather clear. There are atoms that are not coupled to any thermostat. In principle, you can set tc-grps to System and only give one tau and reference temperature and it will work. If you need a more elaborated scheme, them you can supply group definitions (if not available

[gmx-users] Problem running equilibration step

Dear all, I am doing simulation of DNA nano-structure using Gromacs (VERSION 4.6.5) by applying CHARMM26 force field and TIP4P water model. The energy minimization step is working fine but i am facing problem during equilibration step due to wrong *nvt.mdp* file. Can you please guide me, which

Re: [gmx-users] Position restraining of ions.

#ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp

[gmx-users] Analysis of the RMSF of a ligand bound protein structure

Dear all, I am performing MD simulation on a ligand bound dimeric protein structure in Gromacs 5.04. For the calculation of RMSF of this dimeric protein I have used the following command gmx rmsf -s md_0_1.tpr -f md_0_1_traj.xtc -res -o rmsf_res.xvgand selected 'C alpha' group. But the

[gmx-users] Histogram result in free energy calculation

Dear GROMACS users. I have been studying free energy calculation in Justin tutorial. But, I got a somewhat different histogram result compared to the result in Justin tutorial. I uploaded my result files at the following link: http://bio.gnu.ac.kr/~chip/ I don't know why the result is

Re: [gmx-users] Problem running equilibration step

Hello Felipe, Thanks for quick response, I have change my nvt.mdp file according to your instruction, but still getting the following error; Fatal error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values Priyanka On Thu, Jul 16, 2015 at 4:15 PM, Felipe Merino

Re: [gmx-users] How does x2top recognize between alkane C and alkene C

On 7/16/15 12:47 AM, sridhar dwadasi wrote: Thank you for the response. In case of an all atom representation, the connections are different. What about a united atom representation? The g_x2top supports Gromacs 53a5 forcefield right? If you write an .n2t file for it, sure. Can we get a

Re: [gmx-users] Position restraining of ions.

On 7/16/15 6:22 AM, Gordan Horvat wrote: #ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule

Re: [gmx-users] LJ-14 energy

On 7/16/15 7:08 AM, Ming Tang wrote: Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation

Re: [gmx-users] Position restraining of ions.

I should correct myself. Your top file should work too, because grompp assigns certain restraints included in top file to molecules of type defined in the first itp file found above the line that includes these restraints.

Re: [gmx-users] LJ-14 energy

Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation right? Besides, in Gromacs, is the

Re: [gmx-users] Histogram result in free energy calculation

On 7/16/15 3:02 AM, minky son wrote: Dear GROMACS users. I have been studying free energy calculation in Justin tutorial. But, I got a somewhat different histogram result compared to the result in Justin tutorial. I uploaded my result files at the following link:

Re: [gmx-users] Problem running equilibration step

On 7/16/15 7:35 AM, Priyanka Patel wrote: Hello Felipe, Thanks for quick response, I have change my nvt.mdp file according to your instruction, but still getting the following error; Fatal error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values Again, the error is

Re: [gmx-users] Position restraining of ions.

Thanks for the reply. I have one more quick query about position restrain here and its about restraining some pat of the whole protein. Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I would like to set up position restrain in such way that backbone atoms of residues 101-200

[gmx-users] gmx hydorder

Hi gromacs users, I want to use gmx hydorder to get the local tetrahedral arrangement of water surrounding protein within .1 nm . If I understand correctly from this paper in the gromacs manual (P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998)) I think I should get tetrahedrality for each

[gmx-users] g_covar Segmentation fault problem

Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix

[gmx-users] solvation free energy

I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs

Re: [gmx-users] solvation free energy

The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual

[gmx-users] Intel MKL taken in preference of the specified FFT library

Hi, I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU compilers and a self compiled FFTW*. I configured Gromacs with: $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/home/reuti/local/fftw-3.3.4 As there was

Re: [gmx-users] How does x2top recognize between alkane C and alkene C

Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When I represent the connections in n2t file, the

Re: [gmx-users] g_covar Segmentation fault problem

On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated

Re: [gmx-users] How does x2top recognize between alkane C and alkene C

On 7/16/15 12:57 PM, sridhar dwadasi wrote: Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When

Re: [gmx-users] g_covar Segmentation fault problem

Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin

Re: [gmx-users] g_covar Segmentation fault problem

On 7/16/15 1:09 PM, gozde ergin wrote: Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. Then use 4.6.7. Maybe my = should have been instead. The best bet when you get failures like

Re: [gmx-users] g_covar Segmentation fault problem

Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] Position restraining of ions.

On 7/16/15 9:37 AM, anu chandra wrote: Thanks for the reply. I have one more quick query about position restrain here and its about restraining some pat of the whole protein. Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I would like to set up position restrain in such

Re: [gmx-users] g_covar Segmentation fault problem

On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and

Re: [gmx-users] LJ-14 energy

On Thu, Jul 16, 2015 at 1:24 PM Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my

Re: [gmx-users] Intel MKL taken in preference of the specified FFT library

Hi, On Thu, Jul 16, 2015 at 5:47 PM Reuti re...@staff.uni-marburg.de wrote: Hi, I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU compilers and a self compiled FFTW*. I configured Gromacs with: $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1

[gmx-users] there are particles with all coordinates zero

Dear gmx users, I was analysing some trajectories (without any problem), and then just for testing, i used gmx check on them, and i got several warnings: Reading frame3000 time 30.000 Warning at frame 3693: there are 1 particles with all coordinates zero Reading frame4000 time