[gmx-users] Fwd: Dodecahedron Box size and Appropriate number of SOL molecules

, Apramita Chand -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

Re: [gmx-users] Dodecahedron Box size and Appropriate number of SOL molecules

of water molecules should be present in a particular box,right? Regards, Apramita Chand -- 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/Mailing_Lists * For (un

[gmx-users] Confusion regarding creation of .itp file

Hello, I'm a beginner in GROMACS and have been trying to process small molecule topologies through GROMACS for quite sometime. Initially while adding new residues , I thought it's better to modify forcefield files such as ffnonbonded.itp, residuetypes.dat, .rtp entries. However, I've seen in many

[gmx-users] How to build caps for my peptide termini?

Dear All, I want to cap the ends of my peptide chain. Though -ter option of pdb2gmx takes up its zwitterionic form quite easily, I've read somewhere that termini are quite mobile and it is better to proceed with capping. I want to use GROMOS53a6 parameters and I've found entries of ACE and NAC in

[gmx-users] Questions Regarding principal components analysis

Dear All, I have some questions regarding principal components analysis: 1) Is free energy calculations necessary for principal components analysis? I have performed usual MD simulations for my system of a small peptide in solution. If free energy calculations are necessay , I will have to redo

[gmx-users] NPT Equilbration fails

with the specified cutoffs like rvdW=1.4. So I have tried several box sizes and all of them have this problem . I tried changing box type from cubic to dodecahedron but to no avail. What should I do to overcome this problem? yours sincerely Apramita Chand -- Gromacs Users mailing list * Please search

[gmx-users] Fwd: Regarding correct way to calculate diffusion constant

-- Forwarded message -- From: Apramita Chand <apramita.ch...@gmail.com> Date: Fri, Aug 26, 2016 at 6:56 PM Subject: Regarding correct way to calculate diffusion constant To: gmx-us...@gromacs.org Dear All, I want to calculate the diffusion constant of urea in my system.

[gmx-users] Regarding constraints

Dear Gromacs Users, Can I use LINCS constraints instead of SHAKE algorithm while using GROMOS53a6 forcefield? Also, if I want to conduct hydrogen bond property calculations, what should I set the constraint option to in my .mdp file? I'm having the constraint option as 'h-bond' now. Is it right or

[gmx-users] How to calculate radial distribution functions when atoms in different amino acids are named similarly

confusion as to which site is referred to when we mention 'N' or 'C'. So is re-naming the names necessary or is there a way to calculate rdfs with the existing file? Could different index files help? How can we create such index files for different amino acids? Thanking you, yours sincerely, Apramita

Re: [gmx-users] How to calculate radial distribution functions ...(Justin Lemkul)

Dear Justin, Thanks for your reply. I gave a command a O r1 and O atoms from residue 1 were selected as O_r1. Thanking you, yours sincerely, Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Regarding correct way to calculate diffusion constant

a low value for a system conatining 5 urea,751 water and a single protein molecule? Thanking you, yours sincerely, Apramita Chand -- 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

Re: [gmx-users] Structure breaking during minimization

Dear Justin, My .rtp entry for taurine is [TAU] [ atoms ] O3OM -0.607 1 S1SDmso 0.849 1 O1OM -0.607 1 O2OM -0.607 1 C2CH2 -0.039 2 C1CH2 0.376 2 N1NL -0.469 3 H5H 0.368

[gmx-users] Structure Breaking during minimization

Dear All, I'm trying to incorporate charges and topology obtained from ATB server for taurine into GROMOS53a6 ff by copying into my local working directory and adding information in the .rtp file. All other commands work smoothly but after energy minimzation, except for the NH3+ group, all the

Re: [gmx-users] trjconv

Dear Justin,Gregory and Erik, I'd asked earlier whether trjconv might change calculation of properties.For diffusion probably, I could avoid applying trjconv before analysis. For RDF, I checked before and after trjconv, there is a slight difference in the RDFs. For instance , I'm studying a

[gmx-users] Regarding trjconv

Dear All, I had one doubt regarding g_trjconv which I used to center my protein after simulation. I got different diffusion values when I used the .xtc file before and after applying trjconv. Which one should be used? Is trjconv just for visualisation or is necessary for analysis too? Does it

Re: [gmx-users] Regarding trjconv

Dear All, Thanks for your explanation, Erik. I just want to know whether applying trjconv will affect my calculations of other values like radial distribution functions ,hydrogen bond properties. Before applying trjconv,my protein molecule appears to be shifted partly out of the box . Should I be

[gmx-users] Regarding error in hydrogen bond lifetime

Dear All, I'm trying to calculate the hydrogen bond lifetime in my system (water-ethanol) using command g_hbond -f traj.trr -s md.tpr -n index.ndx -ac -life hblife.xvg. It is peculiar to note that when I select index groups as OW and HW (for water), it finds 0 hydrogen bonds! But when I select

[gmx-users] Query regarding hydrogen bond lifetime and energy

Dear All, Is there any way to calculate hydrogen bond energy in GROMACS ? Or at least any information which could be applied from GROMACS to calculate the energy. Also,let me repeat my earlier query. I'm trying to calculate the hydrogen bond lifetime in my system (water-ethanol) using command

[gmx-users] Exactly same rdfs for different residues of protein with water

Dear All, I'm trying to see how the rdf varies for a particular interaction (peptide carbonyl oxygen with hydrogen of water) across different residues. I chose the oxygen atoms belonging to different residues in the index file and also chose the hydrogen atoms from water. To my surprise, all the

Re: [gmx-users] exactly same rdfs for different residues

(aghaei.arsalan) 2. ultrasonic (aghaei.arsalan) 3. Exactly same rdfs for different residues of protein with water (Apramita Chand) 4. Re: ultrasonic (Mark Abraham) 5. Re: ultrasonic (Mark Abraham) 6. Re: Exactly same rdfs for different residues of protein with wat

[gmx-users] Regarding calculation of diffusion constant of solvent molecules near protein surface

Dear All, How would can I calculate how the water molecules near the surface of protein are diffusing? Say I look at some hydrogen bonding interactions using VMD and zoom in and identify the SOL molecules around the surface . Can I create an index file containing those particular SOL molecules

[gmx-users] Regarding g_energy of heterogenous systems

as , for instance : LJ-SR -Protein-SOL - -52.9383 kJ/mol Should it be divided by total number of molecules(protein+sol) to arrive at the value? Please advise. yours sincerely, Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Regarding calculation of diffusion constant (through MSD) of solvent molecules near protein surface

Dear All, Say I want to calculate how the water molecules near the surface of protein are diffusing, how would I do that? Say I look at some hydrogen bonding interactions using VMD and zoom in and identify the SOL molecules around the surface . Can I create an index file containing those

[gmx-users] Unanswered Query regarding hydrogen bond lifetime and energy

> Dear All, > Let me repeat my earlier query. > I'm trying to calculate the hydrogen bond lifetime in my system (water-ethanol) using command g_hbond -f traj.trr -s md.tpr -n index.ndx -ac -life hblife.xvg. It is peculiar to note that when I select index groups as OW and HW (for water), it finds

[gmx-users] Found solution to the problem of same rdfs for different residues

Dear Mark, Thanks a lot for drawing my attention repeatedly to the atom indices I was choosing for making the index file. I chose the atoms using the command 'a O r1' thinking it'll choose the oxygen atom of residue 1. Instead to my surprise,all the oxygen atoms of all residues were selected. I

[gmx-users] Why is Continuous hydrogen bond lifetime so low?

Dear All, The screen ouput HB lifetime usually shows very low lifetime. I've seen from GROMACS Forums that the SHB(t) or continuous lifetime isn't very significant and GROMACS doesn't calculate it very effectively. Any explanations as to why it comes so low? (below 1 ps mostly) Regards Apramita

[gmx-users] Meaning of delta g in hydrogen bond lifetime column

Dear All, Does delta g in hydrogen bond lifetime column mean the enthalpy of breaking the hydrogen bond? I understand it might be derived from the rate constants specified. But can anyone shed light on its physical significance? Regards, Apramita -- Gromacs Users mailing list * Please search

[gmx-users] Regarding grid spacing

Dear All, Which is more appropriate fourier grid spacing for gromos53a6 ff with cutoffs being 0.9 and 1.4nm? 0.16 or 0.12?? I've not seen too many papers with 0.16 being used for this forcefield and that too with cutoffs like 1.0 for rcoulomb and rvdw. Also,should the grid spacing be same for

[gmx-users] Checkpoint files error

Dear All, After equilibration, I want to pass on the checkpoint files state.cpt for production run for which I give the command g_mdrun -s md.tpr -c md.gro -o md.trr -cpi state.cpt -cpo state_md.cpt The job terminates with error that output files for checkpoint files are insufficient Just 1 out

[gmx-users] Regarding grid spacing

Dear All, Which is more appropriate fourier grid spacing for gromos53a6 ff with cutoffs being 0.9 and 1.4nm? 0.16 or 0.12?? I've not seen too many papers with 0.16 being used for this forcefield and that too with cutoffs like 1.0 for rcoulomb and rvdw. Is there any problem if I use fourier

[gmx-users] Grid Spacing

Dear All, Which is more appropriate fourier grid spacing for gromos53a6 ff with cutoffs being 0.9 and 1.4nm? 0.16 or 0.12?? I've not seen too many papers with 0.16 being used for this forcefield and that too with cutoffs like 1.0 for rcoulomb and rvdw. Is there any problem if I use fourier

[gmx-users] In-vacuo minimization of peptide

Dear All, I have constructed the initial structure of peptide using Pymol and energy-minimizing it using steepest-descent algorithm(both with and without restraints) with the conditions: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when

[gmx-users] Which method for choosing concentration is more appropriate

Dear All, This is a general query regarding solvation of peptide in urea-water. My method is to place the peptide in the box first, add urea molecules using g_genbox and then solvate it using water molecules to maintain a desired concentration. There can be two approaches to this: 1) I can keep

[gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

Dear All, Using g_editconf, I am centering the peptide in the box initially. During equilibration, I'm gradually releasing position restraints. I want the peptide to be free to move around so that I might calculate its diffusion constant. In that case, will centering using -c option restrain its

[gmx-users] Problem with center-of-mass RDF and subsequent coordination number calculation

Dear All, I want to calculate the COM RDFs between my peptide and water for which I have used the -com option in gromacs.(Also tried with -com and -rdf res_com). It generates a wierd RDF which does not look correct. I want to take the first minimum and use the -cn option to get the coordination

[gmx-users] Peptide out of box even after applying trjconv

Dear All, Even after applying g_trjconv -f file.gro -s file.tpr -pbc mol -ur compact -center -o newfile.gro, for visualisation purposes of peptide inside the box, a portion of it still sticks out of the box. Is it unnatural? What might be done to sort out the problem? yours sincerely Apramita

[gmx-users] Interpretation of RMSD matrix

Dear All, I would be grateful if you could help me with links to relevant papers/websites/sources on how to interpret RMSD matrices when comparing all frames of single trajectory to reference structure and also when comparing two different trajectories. I am taking the reference structure from

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 27

s.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. RMSD Matrix error (Apramita Chand) >2. Re: EM error (?Mohammad Roostaie? ?) >3. D

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

- only when plateaus are obtained you can begin the > production run) > > Andre > > > On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand <apramita.ch...@gmail.com> > wrote: > > > Dear All, > > *> > I have tested with two ways

Re: [gmx-users] RMSD Matrix Error

Dear Mark, Thanks for your reply. I think you're right about the space needed for generating RMSD Matrix. I definitely was short of 160GB !! Further, you've talked about me using highly correlated frames and that a suitable sub-sampling might solve the problem. How would I know which frames to

[gmx-users] RMSD Matrix error

Dear All, When I'm trying to construct a RMSD matrix , using the command g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m rmsd-matrix.xpm -tu ns I get the error: Last frame 20 time 20.000 Building RMSD matrix, 21x21 elements element 28982; time 2.90 Killed I

[gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Dear All, I have tested with two ways of solvating a peptide with urea-water mixture Method 1: Pre-equilibrating a urea-water box and solvating the peptide with -cs option with this box Method 2: Adding urea molecules to peptide box using -ci option and then solvating the resulting box with

Re: [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)

edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] System reaches ~124K after simulated annealing upto 300K Message-ID: <8fe97070-c577-de07-ba25-64a7230f6...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 6/16/17 10:38 AM, Apramita Chand wrote: > Dear All

[gmx-users] Can we calculate Potential of mean force from normal MD simulations

Dear All, Suppose we have executed a normal MD simulation without using umbrella sampling or pull techniques. If we have the g(r), can we plot potential of mean force between some solutes using this equation? yours sincerely, Apramita -- Gromacs Users mailing list * Please search the archive

[gmx-users] System reaches ~124K after simulated annealing upto 300K

Dear All, I have used the following nvt.mdp file to gradually warm my system upto 300K but just reach upto 124K. I have used variety of options in the simulated annealing like taking less no. of time intervals but in vain Then, I have to perform manually the gradual heating process which takes me

[gmx-users] Fwd: Problem with center-of-mass RDF and subsequent coordination number calculation

Dear All, I want to calculate the COM RDFs between my peptide and water for which I have used the -com option in gromacs.(Also tried with -com and -rdf res_com). It generates a wierd RDF which does not look correct. I want to take the first minimum and use the -cn option to get the coordination

[gmx-users] Fwd: Peptide out of box even after applying trjconv

Dear All, Even after applying g_trjconv -f file.gro -s file.tpr -pbc mol -ur compact -center -o newfile.gro, for visualisation purposes of peptide inside the box, a portion of it still sticks out of the box. Is it unnatural? What might be done to sort out the problem? yours sincerely Apramita

[gmx-users] Setting different intial velocities

the gen_seed. Is this procedure correct? Is there any standard values to pass on to gen_seed or any number will do? Looking forward to your suggestions Thanking you, yours sincerely Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] gmxdump gmxcheck commands not found

, Apramita Chand -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman

[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

a different value than that of the original trajectory value of lifetime.* I would be very grateful for your help. Looking forward to your suggestions Yours sincerely Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] RMSD

steps or before equilibration steps? Thanking you, yours sincerely Apramita Chand -- 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/Mailing_Lists * For (un

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

18 471 4539 erik.markl...@kemi.uu.se <erik.markl...@kemi.uu.se><* *mailto:erik.markl...@kemi.uu.se <erik.markl...@kemi.uu.se>> On 29 Aug 2017, at 07:20, Apramita Chand <apramita.ch...@gmail.com <apramita.ch...@gmail.com><* *mailto:apramita.ch...@gmail.com <apram

Re: [gmx-users] Difference in hydrogen bond lifetimes with and without pbc

Dear Eric and other Gromacs users, Thanks for clarifying about how different timescale of trajectories can affect lifetimes But the case with and without pbc have same length of trajectories (100 ns). Then why the difference in lifetimes ( 1793ps with pbc and 2345 without pbc) Which can be

[gmx-users] Autocorrelation functions for distance vector

Dear All, I want to calculate the time-dependent autocorrelation function for a peptide's end-to-end distance vector . If I use g_dist , it gives me a dist.xvg but though -lt option is there, the lifetime.xvg file is not generated. Is there any command to calculate the autocorrelation function? (

[gmx-users] g_trjorder output

or 1. The problem persists even on increasing the no. of urea molecules to 40 or 80. So is it wrong to add -com option? Considering we're already specifying -da as 0? Yours sincerely, Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Doubts in combination rules 2 and 3

Please clarify these following doubts regarding combination rules in gromos force field: 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are chosen , then are the values converted to sigma and epsilon

Re: [gmx-users] Doubts in combination rules 2 and 3

Dear Justin and David, Thanks for your replies. So as I understand from your answers, I need to put the sigma and epsilon for my atomtypes (without any conversions) under the C6 and C12 columns in ffnonbonded.itp and these numbers will be interpreted as sigma and epsilon when I specify the

[gmx-users] Why do g_trjconv and g_select give different results for the same cut-off

an average of 9-10 solute molecules around reference protein. But when I use g_trjorder , I get 20-23 molecules on an average for the same cut-off of 0.45nm. Any reason why this might be happening? Thanks, Yours sincerely, Apramita Chand -- Gromacs Users mailing list * Please search

[gmx-users] -rerun input trajectory for calculating electrostatic energy

ectory run after production run from the previous simulation done using PME? Thanking you, Yours sincerely, Apramita Chand -- 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.gro

[gmx-users] g_rdf doubts

In g_rdf command, I want to generate rdf between surface of mainchain atoms of peptide and center of mass of solvent molecules so as to compute the distance from the center of mass of each solvent molecule to the van der Waals surface of every atom in the peptide main chain. What should be the

[gmx-users] Error in -rerun

etting the error: *Rerun trajectory frame step 0 time 0.00 has too small box dimensions* after running mdrun Please help me troubleshoot the issue Thanking you, Yours sincerely, Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/M

[gmx-users] Fwd: g_select or g_trjorder

be considered if I want to use these values for calculation of preferential interaction coefficient? -- Forwarded message - From: Apramita Chand Date: Thu, Jun 7, 2018, 3:42 PM Subject: g_select or g_trjorder To: Dear All, I want to evaluate the preferential interaction

[gmx-users] Doubts in visualisation of sdf output

Dear All, I want the SDF of urea as well as water molecules around my peptide molecule. For this purpose , I used trjconv to get traj1.xtc with -fit rot+trans option(selecting peptide as fitting option and system as output). Using this traj1.xtc, I generated traj2.xtc with centering the peptide

[gmx-users] Doubts regarding g_select

Dear All, I am confused between different commands and their outputs for g_select. I want to choose a cutoff of 0.45nm and want to calculate the no. of urea molecules within 0.45 as well as beyond 0.45nm of the peptide backbone. I have a total of 18 urea molecules in my system One of the

[gmx-users] Calculations of preferential interaction coefficient

Dear All, I want to calculate the preferential interaction coefficient and subsequently the Gibbs free energy of solvation for protein in water and in water-co-solvent mixture. 1. According to the equation specified in the literature, if I can generate a list of no. of solvent molecules (for each

[gmx-users] Doubts in g_select and g_trjconv

for water moelcules. But when I add -com option, all of the numebrs decrease to 0 or 1. So is it wrong to add -com option? Considering we're already specifying -da as 0? Yours sincerely, Apramita Chand From: Apramita Chand To: gmx-us...@gromacs.org Subject: [gmx-users] Doubts regarding g_select

[gmx-users] g_select or g_trjorder

Dear All, I want to evaluate the preferential interaction coefficient and according to the equation given in the literature, I want the number of water and cosolute molecules (nw, nx) for local and bulk regions specified by a particular cut-off distance from the protein. There are two options

Re: [gmx-users] Doubts in visualisation of sdf output

...@gromacs.org Subject: Re: [gmx-users] Doubts in visualisation of sdf output Message-ID: <06a53787-59cc-ff56-ae75-28a49c2d6...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 6/4/18 7:05 AM, Apramita Chand wrote: > Dear All, > I want the SDF of urea as well as water molecul

Re: [gmx-users] Doubts in visualisation of sdf output

Dear Justin, Thanks for your reply You're right. I should be choosing a particular density level for all the components. There's another doubt. Why Is it necessary to center the protein before doing g_spatial? Thanks Apramita On 6/4/18 12:04 PM, Apramita Chand wrote: > Dear Justin, >

[gmx-users] Regarding -nmol option

Dear All, In computing interaction energies between groups from g_energy, the -nmol option needs an integer argument that ( as mentioned) should be equal to total no of particles in the system. So if I have a protein-urea-water solution of a single protein, 15 urea and 984 water molecules, for

[gmx-users] Setting correct non-bonded and pair (LJ) parameters in ffnonbonded.itp

to your help, Thanking you, Yours sincerely, Apramita Chand -- 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/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Re Grompp errors while changing combination rules

enerated 1653 of 1653 1-4 parameter combinations" What should be the correct method of changing the ffnonbonded.itp or specifying in the topology file? Please advise. Thanking you, Yours sincerely, Apramita Chand *Message: 4 Date: Tue, 17 Jul 2018 08:1

[gmx-users] Nonbond params and pairtypes section in ffnonbonded.itp

lem. Yours sincerely, Apramita Chand -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth

[gmx-users] Grompp errors while changing combination rules

820) I had taken the exact same system and files with combination rule 1 and the simulation ran smoothly. What could be the problem? Is there anything I have missed out ?Should I use the maxwarn option? Your help will be highly appreciated. Thanking you, Yours sincerely, Apramita Chand

[gmx-users] Per species g_energy value

, should I divide the value by no. of water molecules to get the value per water molecule? Or is it a 'per peptide' value and cannot be divided by no.of water molecules? Please help. Yours sincerely Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Fwd: Per species g_energy value

( coulomb+lr) , should I divide the value by no. of water molecules to get the value per water molecule? Or is it a 'per peptide' value and cannot be divided by no.of water molecules? Please help. Yours sincerely Apramita Chand -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Warning: correlations not long enough

: David van der Spoel To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Warning: correlations not long enough Message-ID: Content-Type: text/plain; charset=windows-1252; format=flowed Den 2018-09-06 kl. 17:13, skrev Apramita Chand: > Dear All, > In my simulations ,I have a Peptide in a

[gmx-users] Hydrogen bond correlations do not start from 1

Dear All, Upon using the g_hbond command with -ac option to calculate forward lifetime,I see that the C(t) does not start from one and keeps varying for different systems like it starts from 0.8 or 0.6 etc... I have tried the normalize flag but to no avail. Will the lifetime output be reliable?

[gmx-users] Warning: correlations not long enough

Dear All, In my simulations ,I have a Peptide in aqueous solution with a cosolvent. For more number of hydrogen bonds like peptide water, water-water, there are no warnings But for Peptide cosolvent, there are 315 hydrogen bonds and it does the acf as 315/315... It shows warning: correlations

[gmx-users] Warning: correlations not long enough

Dear All, In my simulations ,I have a Peptide in aqueous solution with a cosolvent. I'm trying to calculate the forward hydrogen bond lifetime with g_hbond and -ac flag. For more number of hydrogen bonds like peptide water, water-water, there are no warnings But for Peptide cosolvent, there are

Re: [gmx-users] Re Warning- Correlations not long enough

cs.org Subject: Re: [gmx-users] Warning: correlations not long enough Message-ID: Content-Type: text/plain; charset=windows-1252; format=flowed Den 2018-09-07 kl. 17:33, skrev Apramita Chand: > Dear Dr. Spoel, > Initially I used a 100ns simulation with 0.002 time step. > Then I tried a

[gmx-users] Regarding combination rules in gromos53a6 ff

Dear GROMACS users, I want to use the geometric mean of both sigma (sigma i sigmaj)and epsilon(epsilon i epsilon j) as a combination rule in my simulation. According to the combination rules in the manual, the combination 3 incorporates Vii=sigma and Wii= epsilon along with geometric mean of

[gmx-users] Regarding combination rules in gromos53a6 ff

Dear GROMACS users, I want to use the geometric mean of both sigma (sigma i sigmaj)and epsilon(epsilon i epsilon j) as a combination rule in my simulation. According to the combination rules in the manual, the combination 3 incorporates Vii=sigma and Wii= epsilon along with geometric mean of

[gmx-users] Doubt in specifying combination rule

Dear GROMACS users, I want to use the geometric mean of both sigma (sigma i sigmaj)and epsilon(epsilon i epsilon j) as a combination rule in my simulation. According to the combination rules in the manual, the combination 3 incorporates Vii=sigma and Wii= epsilon along with geometric mean of

[gmx-users] Distance vector file for g_analyze: incompatibility of normal and vector

Dear All, I want to generate the autocorrelation function for end-to-end distance vector of my peptide and using g_dist, I have generated a dist.xvg file. On giving this file as input to g_analyze and giving the option -P 1 (for Legendre polynomial), it gives the error: "Incompatible mode bits:

[gmx-users] Settings of SD integrator

sincerely, Apramita Chand -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman

Re: [gmx-users] Settings of SD integrator

Dear John, In the paper, only reference temp has been mentioned Other than that, no additional information is mentioned Can you suggest tau_t values since they are the only settings from that of the case where we use an MD (leap frog) Integrator?? Thanks Yours sincerely Apramita -- Gromacs Users

[gmx-users] Select one molecule closest to another molecule for all snapshots

Dear Gromacs Users, I have two kinds of molecules in my system. I want to know the coordinates of the molecule A that is found closest to molecule B at every snapshot of the MD trajectory. I am using gromacs 5.1. I dont have a cutoff, I just want to generate coordinates of the single one molecule

[gmx-users] Error on scaling the charges

Dear Gromacs Users, I'm simulating an ionic liquid with AMBER 99sb-ildn ff in GROMACS 5.1.4 package. With charges +1 and -1 on the cation and anion respectively, the system is neutral and the minimization is okay. But on scaling the charges by 0.8, the total charge shows to be above 6000, for a

[gmx-users] Regarding too many LINCS warnings for bicarbonate ion

Dear Gromacs users, I am trying to use bicarbonate ions in my simulations employing AMBER99SBILDN ff in GROMACS 5.1.4. For that I've used the antechamber and acpype utilities to generate the parameters for Bicarbonate with RESP charges at HF/6-31G* level of theory. No matter how many times I

[gmx-users] multiple peptide simulation

Dear All, If I have multiple peptides in my system and want to calculate inter-peptide hydrogen bonds, should I group all the peptides separately and calculate hydrogen bonds between every pair of peptide and sum them up? Or calculate overall no. of hydrogen bonds choosing the generic 'Protein'

[gmx-users] gmx spatial error

Dear All, I'm coming across the error "Failed to calloc -9223372036854775808 elements of size 8 for bin" while running gmx spatial. I have three four systems and for the others -nab option with 100 worked fine but here, even after increasing -nab to 1000 , it shows insufficient memory. What could

[gmx-users] Intermolecular interactions in RDF

Dear All, I have 10 peptides in my system and I want to calculate the peptide-peptide radial distribution function. How can I calculate only the intermolecular interactions amongst the peptides (excluding the intramolecular peaks) without repeating the entire simulation? The manual has two options