[gmx-users] gmx_mpi insert-molecules

Dear gromacs users, I want to do md similation of 10 small molecules in water. To this aim, I used following commands: gmx_mpi editconf -f a.pdb -center 0 0 0 -o b.pdb gmx_mpi insert-molecules -ci b.pdb -o c.gro -nmol 10 -box 10 10 10 I have 3 questions: 1) Is my manner true? 2) For 10 molecu

[gmx-users] How to run gromacs on gpu?

Dear all, How to run gromacs on gpu? Which command is required? mdrun? Which options? Best, Shahab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailin

[gmx-users] rtp file

Hi all I investigated dna.rtp file in amber03.ff. There is 4 residue types for adenine: DA5, DA, DA3 and DAN. I know about DA5, DA and DA3. But DAN is unknown for me. Please explain about DAN residue type. Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http:

[gmx-users] residues in force fields

Dear Mark Thanks for your answer. I have a pdb file. If I want to cap N- and C-terminal with ACE and NME, respectively, what to do? Is there an specific software for that? Best wishes, Shahab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

[gmx-users] residues in force fields

Dear all I am a beginner in gromacs. I am studying manual and force fields. I have a question about 2 residue name in aminoacid.rtp file in force fields (for example, amber03). I want to know ACE and NME residues. Any help will highly appreciated. -- Gromacs Users mailing list * Please search

[gmx-users] conversion of amber outputs to gromacs

Dear gromacs users I did md simulation of my system (protein+ligand) using amber. I want to do some analysis using gromacs. In gromacs, I need to xtc and top file for analysis. How do I convert mdcrd to xtc and prmtop to top files? I used AMBER 10 for doing MD simulation. I used amber03 force

[gmx-users] PBC problem in bilayer system

Dear Justin Thanks for your answer. You said " The raw output of g_traj in this case is not very useful " I want to know position and location of drug molecules relative to the DPPC bilayer during simulation time. In your opinion, how should I use this tool (g_traj)? Is g_dist appropriate for

[gmx-users] PBC problem in bilayer system

Dear Justin Very very thanks for your time and consideration. Excuse me for many questions. I want to make sure my trajectory is valid and accurate for analysis and then for writing related paper. My last question is that can I use this trajectory for doing analysis such as g_traj, g_dist, g_d

[gmx-users] PBC problem in bilayer system

Dear Tsjerk Thanks for your reply. I think that there is another problem, except for visualization. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC lipid bilayer (black line) as a function of simula

[gmx-users] PBC problem in bilayer system

Dear Justin Based on your previous reply, I used following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7 When I see **.xtc using vmd, unfortunately, problem was not solved. Please see the following link: https://www.dropbox.com/s/345o7lvc9z4jwln/figure%204.TIF?dl=0 --

[gmx-users] PBC problem in bilayer system

Dear Justin I did following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 Based on your reply*, *I translated all system along the z. I used x and y according to box dimension. I used 9, instead of z dimension (8.30034), for z. When I see **.xtc using vmd, problem w

[gmx-users] PBC problem in bilayer system

Dear Justin I did MD simulation on the NPT ensemble: pcoupl = Berendsen pcoupltype = semiisotropic ref_p = 1.0 In this condition, to solve this problem, what should I do? -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] PBC problem in bilayer system

Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug molecules) are seen in other side of bilayer (bottom).

[gmx-users] PBC problem in bilayer system

Dear Justin you said " The -trans option takes a vector where you specify the amount of translation to apply " I do not know what vector should be considered in -trans option. please guide me to solve this problem as soon as possible. Best, -- Gromacs Users mailing list * Please search the

[gmx-users] PBC problem in bilayer system

Dear Justin Very thanks for your answer. Unfortunately, I am beginner in MD simulation of bilayer membrane systems. Based on your answer (You can try the translation options of trjconv in conjunction with -pbc mol), should I use following command? trjconv –trans –pbc mol trjconv –pbc nojump

[gmx-users] PBC problem in bilayer system

Dear gromacs users When I see trajectory file using vmd, there is state showed in following link: https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0 in initial structure, all 4 drugs were inserted in water phase, in one side of bilayer. Is this state normal? -- Gromacs Users mailing l

[gmx-users] PBC problem in bilayer system

Dear Gromacs users Unfortunately, no one did not answer my previous question about selection of appropriate option for trjconv -pbc to solve pbc problem. For preparation of initial system, I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer

[gmx-users] PBC problem in bilayer system

Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

[gmx-users] PBC problem in bilayer system

Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

[gmx-users] PBC problem in bilayer system

Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or

[gmx-users] search in gromacs mailing list by subject

Hi Before, one could search in gromacs mailing list by subject. But, now, there is not this possibility. Why? Please guide me. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www

[gmx-users] REMD tutorial

Dear Mark Before, in following address you said: Google knows about two GROMACS REMD tutorials. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-January/086563.html Unfortunately, I could not find tutorials you mentioned.

[gmx-users] error with genion

Dear gromacs users I add 4 Cl ions to my system using genion: genion -s ions.tpr -o system.gro -p topol.top -nn 4 -nname CL -nq -1 I encountered with following error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' I checked topolo.top file: [ molecules ] ;

[gmx-users] charged & uncharged ligand

Dear gromacs users. My system contains protein + ligand. Total charge of my protein = 0 My ligand has -NH2 group. I want to do 2 md simulations: 1)deprotonated state of ligand (-NH2). => Total charge of system= 0 2)protonated state of ligand and (-NH3+)=> Total charge of system=+1 I have

[gmx-users] trjorder

Dear Justin Thanks for your reply. My system contains dopc lipid. ns.xtc and ns.tpr files contain all atoms related to dopc molecule. I want to obtain number of atoms in a first group (C38 atom in dopc) which are located in special distance (0.74 nm) of the second group (rest of atoms in dopc).

[gmx-users] trjorder

Hi all I used trjorder -f ns.xtc -s ns.tpr -n ns.ndx -o ns.pdb -nshell ns.xvg -r 0.74 I encountered with Fatal error: An atom number in group is larger than the number of atoms in the trajectory What means of this error? How to fix it? Any help will highly appreciated. -- Gromacs Users mail

[gmx-users] tpr file

Dear Gromacs users I have DMPC + cholesterol + water molecules in my system. grompp tool create *.tpr file containing DMPC + cholesterol + water molecules. But I need a new tpr file only containing hydrophobic chain of DOPC (tail). How to do this? Any help will highly appreciated. -- Gromacs U

[gmx-users] g_order (warning)

Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg I encountered following warnings:

[gmx-users] GridMAT-MD & gnuplot

Dear gromacs users I used GridMAT-MD to obtain area per lipid and bilayer thickness. I used vector for output_format in param_example file. Based on the user guide for GridMAT-MD, when I used gnuplot: perl convert_to_gnuplot.pl output.frame1.20x20.average_thickness.dat 20 20 I encountered wi

[gmx-users] g_order

Dear gromacs users To resolve my previous issue, I used info in the how-to on the g_order page and I checked index file and made a new index file. This time, when I use g_order -s md.tpr -f md.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order.xvg, I encountered following warnings: WARNING: distance

[gmx-users] g_order

Dear gromacs users My system contains DOPC + cholesterol + drug + water molecules. For obtaining deuterium order parameter for the DOPC acyl chains, first, I prepared sn1 and sn2.ndx files. Then I used g_order -s md.tpr -f md.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order.xvg g_order -s md.tpr

[gmx-users] Umbrella Sampling tutorial

Dear Justin When I placed drug within the lipid bilayer, after Generating Configurations step, I obtained 501 gro files. When I used distance.pl script for these gro files, my summary_distances.dat file is as follows: 00.2756352 10.2535359 20.2447009 30.3004653 40.2936225 5

[gmx-users] Umbrella Sampling tutorial

Dear Justin Thanks for your reply If I place drug molecule within the water, can I use the same Pull code parameters in the case drug molecule within lipid bilayer? pull= umbrella pull_geometry = position ; simple distance increase pull_dim= N N Y pull_start = yes

[gmx-users] Umbrella Sampling tutorial

Dear Justin Very thanks for your reply I will slow pulling by changing pull_rate1 from 0.01 to 0.001 and pull_k1 from 1000 to 100. I have a basic question. Before minimization, where should I put drug molecule? into water molecules or into lipid bilayer? Should I put drug molecule in the specifi

[gmx-users] Umbrella Sampling tutorial

Dear Justin My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Based on your suggestion I used pull_geometry = position for my case. After the minimizatio