[gmx-users] grompp

Dear Gromacs users, I am new to Gromacs. I am trying to add ions to my protein system. After typing command: grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o genion_input.tpr where the grompp.mdp contains: ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters

[gmx-users] need you help - New user

(Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:129.307 11.117 0.113213.278 Finished mdrun on node 0 Mon Jun 2 11:00:09 2014 (END) Thank you for your help. Urszula Uciechowska - Ta wiadomość została wysłana z serwera

Re: [gmx-users] need you help - New user

something /Urszula Try using the following command mdrun -v -deffnm nvt On Mon, Jun 2, 2014 at 11:23 AM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear Gromacs users, I am having problem running NVT calculation, when is finished I do not see the *.gro file among

Re: [gmx-users] rlist for implicit water

Dear Justin, How could I change the cut-offs to make the MD more faster in my case? /Urszula On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file

Re: [gmx-users] min in vacuum

Hi gromacs users, I am trying to run coarse-grained MD for a protein system using martini protocol. First step is to run short min in vacuum, whenever I try to do this I am getting an error regarding my input file. ERROR 1 [file system-vaccum.top, line 16]: ERROR: The cut-off length is

Re: [gmx-users] gromacs error

How should I correct the input file? Urszula Uciechowska On 7/31/14, 7:42 AM, Urszula Uciechowska wrote: Dear Gromacs users, I tried to run coarse grained MD however after a few steps I got: Step 39, time 0.78 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.038933

Re: [gmx-users] gromacs error

can rotate before LINCS will complain (END) Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] input error?

= Protein W tau-t= 1.0 1.0 ref-t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau-p= 12.0 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all Urszula Uciechowska

[gmx-users] binding Free energy

Dear gromacs user, I would like to calculate Binding Free Energy Calculations for my protein-DNA complex (already run for 50ns). Is there any manual or tutorial (for more complex systems) available? best regards Urszula - Ta wiadomość została wysłana z

Re: [gmx-users] question about walls for a simple water box

for 50ns and I was extending my simulations every 10ns. Any suggestions? best regards Urszula Uciechowska --- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland

[gmx-users] combine tpr files?

for 50ns and I was extending my simulations every 10ns. Any suggestions? best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] MD for DNA structure

Dear Gromacs users, I am trying to run MD for my DNA structure, however after typing grompp -f nvt.mdp -c em.gor -p top -o *.tpr I am getting an error message: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# NOTE 1 [file nvt.mdp]: The Berendsen thermostat does not generate the

[gmx-users] hbond analysis

trajectory and run hbond anlysis in ptraj? or can I convert it somehow? Best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość

Re: [gmx-users] hbond analysis

Dear Gromacs users, Regarding the g_hbond analysis. What does exactly represent the second and third column in hbond.xvg file (pasted below)? g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bonds @xaxis label Time @yaxis

[gmx-users] ramachandran plot

Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta

Re: [gmx-users] ramachandran plot

, 2014 at 4:31 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Could you please send me the code? It can be on my private email. Thanks a lot Ursuzla Hi Urszula, It's a while ago that I made that one, and I don't have the code at hand. But it's a combination

Re: [gmx-users] ramachandran plot

() #---End of image--- On Mon, Nov 17, 2014 at 1:44 PM, Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Dear Tsjerk, Could you send me the script again? as I did not find the attachment in your previous email. best regards Urszula Hi Urszula, Attached is an R script

[gmx-users] dihedral angle g_angle?

HI I use mk_angndx to produce angle.ndx then, I entered g_angle -od angdist.xvg -ov angaver.xvg -type dihedral it follows the options: Group 0 ( Phi=0.0_3_0.60) has 368 elements Group 1 ( Phi=0.0_2_4.92) has 368 elements Group 2 ( Phi=0.0_3_0.65) has 1104 elements

Re: [gmx-users] DNA-protein complex

of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain best regards Urszula Uciechowska 2015-03-17 14

[gmx-users] DNA-protein complex

Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? Thank you in advance for your suggestions. best regards Urszula - Ta wiadomość została

[gmx-users] Fatal error

Hi, I am trying to run pdb2gmx by using: pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ignh -water tip3p -ter however I am getting a fatal error: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pgutil.c, line: 99 Fatal error: Atom

[gmx-users] How to run pdb2gmx with -ter flag?

while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- How to run it correctly? Urszula Uciechowska University of Gdansk and Medical

Re: [gmx-users] How to run pdb2gmx with -ter flag?

for me. Thank you for your help Urszula Hi, -ter does not solve this problem. You should not start new work with such an old version of GROMACS; I forget when we added -chainsep, but it solves this problem. Mark On Wed, 6 May 2015 15:37 Urszula Uciechowska urszula.uciechow

[gmx-users] error gcq#360

Dear gmx users, after running grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr I obtained: GROMACS: gmx grompp, VERSION 5.0 Executable: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/bin/gmx Library dir:

[gmx-users] GMXPBSA

Dear gromacs users, I would like to run BFE calculations with gromacs. I performed MD simulations for 100ns and would like to extract snapshots from the MD and split them into the complex, protein and DNA. My question is how many sps should I extarct from the MD? and Are there any scripts

[gmx-users] input file

Dear gmx users, I am using 5.0.6 version. After running the: grompp -f ions.mdp -c caulob-mod-it_solvated.gro -p caulob-mod-it.top -o ions.tpr NOTE 1 [file ions.mdp, line 16]: ions.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with

[gmx-users] tutorial

is the traj_helix.xtc? Thank you in advance for your help. best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana

[gmx-users] tutorial

is the traj_helix.xtc? Thank you in advance for your help. best regards Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana

[gmx-users] chainsep in pdb2gmx

for any advice best Ula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland - Ta wiadomość została

[gmx-users] fatal error

2.302 19.107 3.565 1.00 72.46 C What can be wrong with the P atom? Thanks for any suggestions. best Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing

Re: [gmx-users] fatal error

Hi, I do not know. After running pdb2gmx I am not getting the .itp file for the DC5... I am using gromacs 5.0.4. What can be wrong here? Urszula > Hi, > > What name does the .rtp entry for DC5 use for its phosphorus atom? > > Mark > > On Mon, Mar 6, 2017 at 1:39 P

[gmx-users] REMD implicit solvent

of equilibration step. I appreciate any recommendation. Thanks Urszula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland

Re: [gmx-users] REMD implicit solvent

Thanks >> Ula >> >>> Hi, >>> >>> Did you try to debug your setup by running a normal single-replica >>> simulation first? >>> >>> Mark >>> >>> On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < >>> urszula.ucie

Re: [gmx-users] REMD implicit solvent

website at http://www.gromacs.org/Documentation/Errors Any suggestions? What can I do to run it? Thanks Ula > Hi, > > Did you try to debug your setup by running a normal single-replica > simulation first? > > Mark > > On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechow

[gmx-users] phi/psi

Hi, How to get phi/psi angles from gromacs trajectory file? I used v.4.5.5. best Urszula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland