[gmx-users] How to find free energy barrier from FEL which generated from dPCA?

Dear Gromacs users, I have generated the FEL from dPCA of 20 residues length of peptide. I check the fel.txt file which was used for the FEL generation in mathmatica. I was not able to find the energy barriers from the FEL. I request you to guide to how to find the free energy barriers from this FE

[gmx-users] How to generate force field for carboxylated lysine residue?

Dear gromacs users Sorry for my previous email which has been sent by mistakenly. Coming to my problem, I have a protein which has carboxylated at N epsilon position of Lysine. I have gone through the many force fields and I did not find any force field which represents the carboxylated lysine. T

[gmx-users] how to generate force field for carboxylated lysine?

Dear gromacs users I have a protein which has carboxylated at N epsilon position of Lysine. I have gone through the many force fields and I did not find any force field which represents the carboxylated lysine. Then I got the topology file for carboxylated lysine ATB server. Now I have many questio

[gmx-users] Can I take any conformational sub state from REMD

Dear gromacs users I have 20 residues length of peptide and it has some helix content. I have done REMD (with lower temperature range 300K and upper temperature 450K) to denature the helix. I gave desired exchange probability 0.25 and I got 30 temperature points and I did REMD simulations all 30

[gmx-users] FEL generated by dPCA and radius of gyrationa vs RMSD

Dear gromacs users, I have generated free energy landscape by two methods such as dPCA and radius of gyration vs RMSD to average structure. In dPCA I got less number of meta conformational states than radius of gyration vs RMSD method. Can I use the second method for my paper submission? Thanks

[gmx-users] Methodology of dPCA

Dear gromacs users, I am Surya a Ph.D. scholar from lab of computational biology, CDFD, Hyderabad. I have done simulations for 100ns of 20 residue length peptide. I have done dPCA as mentioned in the gromacs tutorial. I have made a dangle.ndx file with all dihedral angles atom numbers. I create

[gmx-users] I have not been able to do dPCA

Dear gromacs users, I would like to do dihedral PCA for my 20 residues trajectory. As I have interested in first 10 residues of my peptide, I have generated the .ndx file which has the dihedral atoms of first ten residues. Then I executed the following command. gmx_mpi angle -f md_0_1.xtc -s md_

[gmx-users] how to use fastpca?

Dear gromacs users, I have installed fastpca to do the dihedral principal component analysis. But I am not getting how to use the fastpca. If anybody used this tool to do dPCA, let me know how to do it. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please searc

[gmx-users] Regarding DPCA

> Dear gromacs users > > I done simulations of peptide of 20 residues length for 300ns. As I would > like to explore the conformational flexibility I have chosen to do dPCA. I > have gone through the tutorial which is present in the gromacs cite. > Firstly, I have created the index file which shows

[gmx-users] cannot successfully finished the dPCA

Dear gromacs users I done simulations of peptide of 20 residues length for 300ns. As I would like to explore the conformational flexibility I have chosen to do dPCA. I have gone through the tutorial which is present in the gromacs cite. Firstly, I have created the index file which shows the dihedr

[gmx-users] how to do dPCA

Dear gromacs users, I have done simulations of 20 residues length peptide for 300ns. As I would like to do explore the conformational space I have chosen the dPCA to find flexible regions. I have gone through the dPCA tutorial from gromacs site and followed it. First I have generated the index fi

[gmx-users] unable to understand dPCA

Dear gromacs users, I have done simulations of 20 residues length peptide for 300ns. As I would like to do explore the conformational space I have chosen the dPCA to find flexible regions. I have gone through the dPCA tutorial from gromacs site and followed it. First I have generated the index fil

[gmx-users] Hydrogen bonds for particular residue during simulations.

Dear gromacs users, I have done simulations of 20 residue length of peptide for 100ns. I want to find hydrogen bonds for residue GLU-7. The topology information for this residue as follow. ; residue 7 GLU rtp GLU q -1.0 121 opls_238 7GLU N 39 -0.514.0067 ; q

[gmx-users] water molecule cannot be settled during minimization!!!!

Dear gromacs users I am trying to simulate one protein with 180 residues. During energy minimization I got the falling error. Fatal error: step 26: Water molecule starting at atom 28787 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have reduced the em s

[gmx-users] how to do neutralization?

Dear gromacs users I got the system non-zero total charge: -0.226000. When I add one NA ion to the system I got non-zero total charge: +0.77. What is the way to neutralize the system? Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at h

[gmx-users] force field for selinomethionine?

Dear gromacs users, I have to do simulations for a peptide which has the selinomethionine. But regular force fields from gromacs has no information for this residue. kindly give me information if is there any force field for selinometheoinine. Thanks in advance Surya Graduate student India. -- G

[gmx-users] how to do dPCA?

Dear gromacs users I would like to do dPCA for my 100ns trajectory. When see in the gromacs tutorial I could not create the covar.ndx file. My peptide is 20 residues length. I made .ndx file for dihedral angles and after generating the dangle.trr file. But here I have one problem, to generate the

[gmx-users] Whether my simulation is conserved?

Dear gromacs users, I have done simulations for 100ns. To know whether my simulation is conserved, I have preferred to do simulated annealing. I have set the highest temperature as 350K at 25ns and allowed it go down to room temperature 300K at 50ns. And eventually I executed the mdrun for 50ns at

[gmx-users] successive removal of position restrain?

Dear gromacs users, I have gone through one gromacs tutorial of md simulation in solvent. Where they mentioned that successive removal of position restrain. In other words first they have done NPT ensemble with 1000 1000 1000 energy constants, then re executed the NPT ensemble with 100 100 1

[gmx-users] Showing different RMSD values

Dear gromacs users I have done simulations for 100ns two times with similar conditions of 20 residue length peptide. I have plotted the RMSD graph. The average RMSD values for simulations are 0.486 and 0.4102. My question is why I didn't get similar average RMSD values even though the conditions f

[gmx-users] Error in simulated annealing

Dear gromacs users, I wanted to do simulated annealing and I set up the .mdp file as follow... title = OPLS 4qam MD simulation define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 500

[gmx-users] Setting up SA

Dear gromacs users, I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simulated annealing (SA). Then I have gone through the simulated annealing notes which I found on gromacs web

[gmx-users] Simulated annealing

Dear gromacs users, I am extremely sorry for my previous incomplete mail. By mistaken I have pressed some short cut key. I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simul

[gmx-users] setting up simulated annealing

Dear gromacs users, I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simulated annealing. Then I have gone through the simulated annealing notes which I found on gromacs website

[gmx-users] Difference in omega angles!!

Dear gromacs users First I have done simulations of peptide for 100ns. And then I have generated the .pdb file after energy minimization by following commands executed. gmx trjconv -s em.tpr -f em.trr -o em.pdb After generation of PDB file, I did mutation at one position in em.pdb file and named

[gmx-users] evaluation of simulated frames by procheck

Dear gromacs users, I have done simulation of peptide with 28 residues length for 100ns. I have used the OPLS force field. My peptide is disordered peptide and two of its regions have been modeled by using modellar. After modelling I have checked the steriochemical properties of the peptide by pr

[gmx-users] No procheck output for md starting structure.

Dear gromacs users, I have done simulations for 100ns. When I have checked the stereo chemical properties for my starting structure by PROCHECK, I didn't get any ramachadran plot. I have got the starting structure by executing the following command. "gmx trjconv -s md_0_1.tpr -f md_0_1_noPBC.xtc

[gmx-users] Has omega -180 also in proteins?

Dear gromacs users, I have done simulation for 100ns and I analyzed many properties as part of my work. I also calculated the omega dihedral angle and I got the values around +180 and -180 degrees. When I present the work in lab they questioned about the omega values of PROLINE. It should be ar

[gmx-users] how to get omega angles for a trajectory?

Dear gromacs users, I would like to compute omega angles for a trajectory which I have simulated. when I use "gmx chi" command I got some 5 column data with S1 S2 para meters. I didn't understand that data. Kindly tell me how do I get omega angles for trajectory? Thanks in advance Surya Graduate s

[gmx-users] Doubt in RMSD

> Dear gromacs users, >> >> I have done simulations for 100ns. My peptide length is 25 residue length. >> While calculating the RMSD by executing the gmx rms I have used 2 C-alpha >> atoms at N-terminal and one C-alpha atom at C-terminal for least square >> fitting and then calculated the RMSD for

[gmx-users] Doubt in RMSD

Dear gromacs users, > > I have done simulations for 100ns. My peptide length is 25 residue length. > While calculating the RMSD by executing the gmx rms I have used 2 C-alpha > atoms at N-terminal and one C-alpha atom at C-terminal for least square > fitting and then calculated the RMSD for the res

[gmx-users] doubt in RMSD

Dear gromacs users, I have done simulations for 100ns. My peptide length is 25 residue length. While calculating the RMSD by executing the gmx rms I have used 2 C-alpha atoms at N-terminal and one C-alpha atom at C-terminal for least square fitting and then calculated the RMSD for the rest of the

[gmx-users] How to find free energy barriers between conformational sub-states of simulation?

Dear gromacs users, I have done simulations of 20 residue length peptide for 100ns. I have performed clustering and got some 29 clusters. Now would like to calculate the free energy difference between these clusters. kindly tell me how to find the free energy difference between the clusters. Than

[gmx-users] How to resolve OXT atom issue?

Dear Justin, I apologize you as I am wasting your valuable time. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When

[gmx-users] How to solve OXT atom (termial oxygen atom) issue?

First of all I am extremely sorry for my mistake. I haven't sent you the modified coordinate file. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen ch

[gmx-users] How to solve the terminal oxygen atom issue (OXT atom) ?

Dear gromacs users, I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When I executed the pdb2gmx I got following error. Fata

[gmx-users] How to solve the OXT atom (terminal O atom) issue?

Dear gromacs users, I have peptide with 68 residues and some of the SER and THR residues are phosphorylated. I have chosen charmm36 force field. When I executed the pdb2gmx I got following error. Fatal error: Atom OXT in residues GLN 68 was not found un rtp enrty GLN with 17 atoms while sorting

[gmx-users] Force filed for phosphorylated residues

Dear Mark, I have used the charm36 force field. In c.tdb following atoms are there. ; CHARMM CTER [ COO- ] [ replace ] C C CC12.011 0.34 O OT1 OC15.9994 -0.67 OXT OT2 OC15.9994 -0.67 [ add ] 28OT C CA N OC 15.4 -0.67-1 [ impropers]

[gmx-users] Force field for phosphorylated residues

Dear gromacs users, I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me

[gmx-users] forcefield for phosphorylated residues

Dear gromacs users, I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me what

[gmx-users] story behind the PCA

Dear gromacs users, I have gone through many tutorials and I didn't get much about principal component analysis(PCA) in gromacs. Kindly some one tell me the story behind the PCA and whats the relation between PCA and free energy landscape? Thanks in advance Surya Graduate student India. -- Groma

[gmx-users] doubt in PCA?

Dear gromacs users, I just want calculate the free energy difference between two successive trajectories. As I know first we have to generate contrivance matrices by using gmx covar and then have to execute the gmx anaeig for eigenvector analysis. Here my doubt is how to give my interest of traject

[gmx-users] how to find energy barrier between two cluster centroids?

Dear gromacs users, I have done 100ns simulation for a peptide with 50 residues length and I generated clusters. Now I would like to calculate the energy difference between two cluster centroids. I have gone through some tutorials and I could not find how to find free energy difference. Kindly tel

[gmx-users] RMSD of energy minimized structure

Dear gromacs users, I have done energy minimization of clustered PDBs. When I try to calculate the RMSD between the minimized clustered PDB and the starting structure of MD simulations I got the following warning. If there are molecules in the input tarjectory file that are broken across periodic

[gmx-users] How to fix RMSD cutoff in clustering

Dear gromacs users, After my 100ns simulation I want to do clustering. When I look into the gromacs functions I got gmx cluster. This function do clustering based on RMSD cutoff. I searched literature for how to fix RMSD cutoff. I could not find it. Kindly tell me on which criteria we can fix the

[gmx-users] energy minimization

Dear gromacs users, I have done simulations for 100ns. I would like to do energy minimization by using trajectory file which I got after production phase. Can I do energy minimization passing the trajectory file to -c argument? If it is yes, then tell me how to do it. Thanks in advance Surya Grad

[gmx-users] Interest of c alpha atoms for least square fitting?

Dear gromacs users, Can I give my interest of c alpha atoms for least square fitting in gmx rms for RMSD calculation? Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Doubt in gmx rms

Dear gromacs users I have executed the following command for the calculating the RMSD of a protein. gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx My doubt is whether I did correct or wrong I don't know. I have simulation of 197 residues length protein and I want to ca

[gmx-users] how does gmx rms work?

Dear gromacs users, Previously I posed a problem how to calculate the RMSD of our interested region of protein, even though I did simulation for full length protein. I got solution from one of our user. Based his suggestion I created index file and have executed the following command. gmx rms -s

[gmx-users] RMSD of interested region?

Dear gromcas users, I have done simulations for 100ns for protein of my interest. The protein length is 197 residues and I fixed the positions one n-terminal residue and from 28th residue to 197 residues also fixed. My interest of area in protein is from 2 to 27 residues. Although I have done simu

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 102

an vary independently and is usually > applied > to crystals or other solid materials. Coupling xy and z separately is > semiisotropic and is usually used with membranes and surfaces. For a > simple > aqueous protein system, isotropic is in fact correct. > > -Justin > >

[gmx-users] Fwd: The results of your email commands

advance Surya Graduate student India. - Done. -- Forwarded message -- From: Seera Suryanarayana To: gmx-users-requ...@gromacs.org Cc: Date: Sat, 27 Aug 2016 12:39:45 +0530 Subject: How to do position restrain to particular residues? Dear gromacs users, I want to do

[gmx-users] Segmentation fault

Dear gromacs users, I have done mdrun for 10ns with position restrain of interest of our residues. Here I woulk like to explain how I did the position restrain. During gmx pdb2gmx command we usually get posre.itp file which we use in the equilibrium process to restraint the protein. As I want to

[gmx-users] g_cluster or g_clustsize

Dear Gromacs Users, I would like to do clustering of my trajectories. When I look into gromacs tool for clustering, I got g_cluster which is based on the RMSD and the other one is g_clustsize which computes the size distributions of molecular/atomic clusters in the gas phase. Mine is protein in so

[gmx-users] gromcas installation

Dear users, I have centos 6.6 server with 64 processors. I want to do parallel simulations by enabling the MPI threads. For installation of gromacs can I follow the typical gromacs installation guide which is available in the installation instructions? Thanks in advance Surya Graduate student Ind

[gmx-users] protein has broken after 100ns simulation

Dear gromacs users, I have simulated protein for 100ns. When I visualized the protein in VMD, I have seen the protein into different fragments. Later I came to know that there is no breaking phenomena in simulations and that is because of the PBC problems. I have executed the trjconv command with

[gmx-users] Extension of simulations

Dear users, I have extended my simulations from 20ns to 40ns and I concatenated the .xtc files by using trjcat. I would like to use the concatenated file for further analysis such as rmsd and radius of gyration. We need to have two input files for rmsd analysis. one is .xtc(trajectory file) and ot

[gmx-users] Problem in rmsf calculation

Dear gromacs users, After mdrun I have plotted the rmsf for C-alpha atoms. My protein has 143 C-alpha atoms and I expected only that number in the plot. But I got rmsf values for all atoms of the protein(more than 2250 atoms). I have attached the plot for more information. What could be the reaso

[gmx-users] How to fix the ends of the protein?

Dear Gromacs users, I would like to simulate the topological domain of one protein. For that I need to fix the ends of the simulated protein. How do one can fix(constraint) the ends of the protein? Kindly help me how to do this fixation? Surya Graduate student India. -- Gromacs Users mailing lis

[gmx-users] Introduction of mutation into a PDB file, how?

Dear Gromacs users, I would like to introduce mutation into a pdb file which is going to be used for md simulations. Kindly suggest me the software otherthan SPDV. thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

[gmx-users] Encountered with error after executing the command "gmx solvate"

Dear gromacs users, I have been trying to simulate the xtal structure which is homo tetramer and each chain has more than 400 amino acids. after editconf where I have used the cubic box with -c -d 1.0. After this command I have executed the following command.. gmx solvate -cp 4pv1.gro -cs spc216.

[gmx-users] How to fix miising atoms in a pdb file?

Dear gromacs users, I have one pdb file which does not have one atom and I need to be fixed that atom in the pdb to run MD simulations. Kindly suggest me to how to fix it. Can I mutate the residue of my interest with the same residue by using pymol or SPDBV to fix the missing atoms? Thanks in Adv

[gmx-users] (no subject)

Dear Gromacs Users, Sorry for the same mail again. I haven't provide sufficient information in previous mail. After energy minimization I have done nvt equilibrium for 1ns. It has taken 15 to 20 minutes when I done it previously. Same equilibrium I did day before yesterday and it has take almost

[gmx-users] Getting too much time to finish nvt equilibrium, why?

Dear Gromacs Users, After energy minimization I have done nvt equilibrium for 1ns. It has taken 15 to 20 minutes when I done it previously. Same equilibrium I did day before yesterday and it has take almost one day. I have used the same work station in both equilibrium processes. I have used the f

[gmx-users] Warning in the em.

Dear Gromacs Users, After my energy minimization I got the following info. I would like to know does it mean. I came to know that my em process is not perfect. Kindly tell me how resolve this problem. Energy minimization has stopped, but the forces have not converged to the requested precision F

[gmx-users] Script to submit the md simulations on cluster.

Dear gromacs users, I would like to submit the mdrun on cluster. I have written a shell script for submission as following. EXECUTABLE=./mdrun_mpi465 ARGUMENTS = -v -deffnm md_0_1.tpr INPUT_FILES = file:///home/suryanarayana1599/md.mdp, file:///home/suryanarayana1599/npt.cpt, file:///home/suryana

[gmx-users] End to end fixing

Dear Gromacs users, I have one protein which has the topological domain with two trans membrane domains. I would like to simulate the topological domain present in the cytosol. But here I can't do simulations as normals proteins. Because as the topological domain has trans membrane domains both si

[gmx-users] Can't load converted trajectory on to vmd

Dear gromacs users I have executed the trjconv command for generating the .xtc file to futher analysis. I have selected protein for output. I loaded the .gro file on to vmd and then I tried to load .xtc file on to vmd. But, I couldn't load it and I got the following error. vmd > Info) Using plug

[gmx-users] How to remove the water molecules?

Dear gromacs users I have simulated a protein for 500ns in solvent system. I want to remove water molecules from the system to further analysis. I have gone through the manual, but I couldn't find how to remove water molecules. Kindly tell me how can I do it. Thanks in Advance Surya Graduate stude

[gmx-users] During mdrun my protein moves towards edges

Dear gromacs users I have been running the real mdrun after equilibration. mdrun has been submitted for 500ns. After some time(150ns) the protein moves towards edges. I want the internal moments only, but whole protein moves all sides of box rather than at centre of the box. Kindly tell me how to

[gmx-users] How do we calculate free energy of simulated protein

Dear gromacs users I would like to calculate the free energy of simulated protein, how does it can be done? Surya Graduate student India. -- 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

[gmx-users] Unable to install gromacs

Dear Gromacs Users We have been trying to install gromacs-5.0.4 on ubuntu 14.04 work station. We have installed all the prerequisites for the gromacs and whenever exicuting the cmake .. we got following error. - The C compiler identification is unknown -- The CXX compiler identification is unknow

[gmx-users] Define box size

Dear gromacs user I have one protein with 254 residues. I would like to simulate this protein in solvent system. For that first we need to define box by editconf. My question is how does we define box size? Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive a

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 1

> than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: Electrostatic force cutoffs (Mark Abraham) >2. Position Restraint or remove COM from DNA (Hovakim Grabski) >3. Re: Position Restraint or remove COM from DNA (Justin Lemkul)

[gmx-users] Why the rmsd value has been varied from different hardware for same protein?

Dear Gromacs Users I have done simulation of one protein in different computers such as GPU(tesla C2075), cpu and cluster(two different nodes with 32 processors) for 5ns. I got different rmsd values for the same protein, but I used same minimized structure in all the computers. My question is what

[gmx-users] Can we calculate rmsd from after energy minimization?

Dear Gromacs Users I would like to know whether it possible to calculate rmsd immediately after energy minimization step, in other words from em.tpr and em.trr file. I tried to calculate the rmsd by using above mentioned files, but I have got nothing. If it is possible to calculate the rmsd fro

[gmx-users] How to overcome the error "Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom."

Dear gromacs users I have been tried to simulate the protein-dna complex. I got error as "Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom" upon using the command pdb2gmx. I have been added the P atom and bonds of P in the .rtp file which is the part of A

[gmx-users] Long bond streches during simulations

Dear gromacs users I have done mdrun upto 50ns by using the command "gmx mdrun -deffnm md_0_1 -nt 7. I have total 8 threads and I used 7 out of it along with graphic card nvidia tesla 2075. I first thing I would like to know that when I load the .trr or .xtc file after the .gro file into the vmd

[gmx-users] How to save trajectories of our interest into vmd

Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- Gromacs Users mailing list * Please sear

[gmx-users] OpenMM Compatibility issues with GPU build

Dear Gromacs users, I have successfully installed a) cudatoolkit_4.2.9_linux_64_ubuntu11.04.run b) devdriver_4.2_linux_64_295.41.run c) gpucomputingsdk_4.2.9_linux.run d) OpenMM 4.1 from Source e) GROMACS 4.6.5 While trying to install / cmake of mdrun-gpu using the standard procedure given in GR