[gmx-users] g_analyze

Dear all When I use the following command: g_analyze -ffree_bi_0.9.xvg -av average_0.9 I got set average standard deviation *std. dev. / sqrt(n-1)*… SS16.053822e+01 3.062230e+01 1.936724e-02… What is “*std. dev. /

[gmx-users] Standard errors

Dear all I would like to calculate the standard deviation (as the error bar) for dV/dlanda.xvg file. I used g_analyze command as the following: g_analyze -ffree_bi_0.9.xvg -av average_0.9 I got: set average *standard deviation* *std. dev. / sqrt(n-1)

[gmx-users] Error bar for free energy

Hi Dear Gromacs users, I would like to calculate the standard deviation (as the error bar) for dV/dlambda.xvg file. I used g_analyze command as the following: g_analyze -ffree0.9.xvg -av average_0.9 I got: set average*standard deviation**std. dev. /

[gmx-users] Invalid order for directive atomtypes

Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct graphite.itp file. Generated topology file is as the following: #include ./oplsaa.ff/forcefield.itp #include TP.itp

[gmx-users] atomtypes in .n2t

Dear users To generate a topology file for an arbitrary molecule, I used g_x2top program. I added following lines to atomname2type.n2t: .. .. C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149 C opls_145B 0.091698 12.0110 3 C 0.149 C 0.1395 C 0.1395 .. But,

[gmx-users] .n2t file format

Dear gmx users I scrap lines from some files in oplsaa.ff folder as the following ffnonbonded file: [ atomtypes ] opls_157 CT6 12.01100 0.145 A3.5e-01 2.76144e-01 atomtypes.atp file: opls_157 12.01100 ; all-atom C: CH3 CH2, alcohols also, I looked at

[gmx-users] Generate topology

Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM

[gmx-users] Generate topology

Dear Justin thanks for your reply, I did it. when I put the .n2t in my working directory,I have gotten this error. thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Generate topology -2

Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM

Re: [gmx-users] Generate topology

. Afsaneh On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 8:53 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1

[gmx-users] Adjust time intervals

Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same.

Re: [gmx-users] Adjust time intervals

of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got

Re: [gmx-users] Adjust time intervals

Dear Justin, I use version 4.0.7 Thanks Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. Which

Re: [gmx-users] g_sas

can get from The SAS_calculations of residue protein in two ways? Best wishes, Afsaneh On 3/15/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s

[gmx-users] g_sas; could not find a Van der Waals radius

Hi, I have a system that is contained of Protein-DOPC-SOL-Ions. I want to calculate residue SAS of protein.The calculation group consists of all the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14 ion),and then protein for output. Force files used for protein and DOPC are ffg53a6

[gmx-users] g_sas

Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area

[gmx-users] g_sas

Dear user, I have a system that is contained of protein-water-ions. There, I select the whole protein first for calculation, and then this protein for output. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc In this way I can obtain

Re: [gmx-users] g_dist without output file

On 3/10/12, lina lina.lastn...@gmail.com wrote: On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina There is not any things related to list of atoms on the terminal. Might your distance -dist so large. try a smaller one and see. Best regards --

[gmx-users] Warning: g_sas Vdwradii.dat

Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Justin. I had not added van der Waals of phosphor for phosphor in vdwradii.dat, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following warning:

[gmx-users] g_sas vdwradii.dat

Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following

Re: [gmx-users] Coulomb Energies

On 12/17/11, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote: Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error

[gmx-users] do_dssp

Hi, I'm trying to use do_dssp of gromacs 4.5.4 in fedora core . I did processes of Download , Uncompress and Compile the source code as the following unzip dsspcmbi.zip cd dssp [root@localhost dssp]# ./DsspCompileGCC That i got this message: Running script to compile the CMBI version of

[gmx-users] How to install FFTW 3.2.2

Hi, To compile a single-precision version of the libraries and install FFTW version 3.2. I followed the steps inhttp:// www.gromacs.org/Downloads/Installation_Instructions#Prerequisites . my computer characteristics: Root at …fftw-3.2.2]# uname -a Linux localhost.localdomain

[gmx-users] How to install gromacs 4.5.1

Hi, My characteristics computer: Root at …fftw-3.2.2]# uname -a Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux To install FFTW version 3.2.2. I used the following commands: Root at …fftw-3.2.2]# ./configure

[gmx-users] Contribution of delta bonding energy in the delta free energy

Hi, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs energy. Best wishes, Maleki, -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Contribution of delta bonding energy in the delta free energy

at 6:18 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/08/2011 9:13 PM, afsaneh maleki wrote: Hi, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs

[gmx-users] Vectors in non-cubic box

Hi, I want to create *.gro file with simulation box size as following: 3.460467452 0. 0. 1.730233726 2.9968527222000 0. 0. 0. 10.00 I used the command: ]editconf –f *.pdb –o

Re: [gmx-users] Vectors in non-cubic box

Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] pressure coupling not enough values (I need 2)

Hi, grompp show the error as below: ERROR: pressure coupling not enough values (I need 2) I used ref_p =1. In file.mdp How to solve this problem? thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] dgdl.xvg file

Hi, Is there command in .mdp to adjust of frequency to write dg/dlamda to dGdL.xvg file? I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do? thaks in advance, Afsaneh Maleki -- gmx-users mailing

[gmx-users] Overriding atomtype O

Hi, I have a problem with grompp. I want to simulate membrane protein. I adjust the [ molecules ] section to list the number and type of my components I run grompp and it shows 56 warning about all of atom types in ffG53a6nb.itp (56 atom types are in ffG53a6). I run pdb2gmx for protein

[gmx-users] dgdl.xvg

Hi, Is there command in .mdp to adjust of frequency to write dg/dlamda to dgdl.xvg file? I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do? Thanks in advance. thanks very much, Afsaneh --

[gmx-users] moleculetype CU1+ is redefined

Hi, When I generate the tpr file with grompp, I get the following error. Fatal error: moleculetype CU1+ is redefined I work on membrane protein that have no atomtype CU1+. why i get error on CU+? I have cheked [moleculetypes] in toplogy file and there are n't doplicated. How to remove this

[gmx-users] ions.itp

Dear justin, thanks for your helpful reply. where Gromacs does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. why in ions.itp #ifdef _FF_GROMACS is defended? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: moleculetype CU1+ is redefined

this error is removed. becuse ion.itpwas included twice in .top and .itp files. i have included two FF into topology file, one for protein and another one for bilayer. Afsaneh On Mon, Jun 14, 2010 at 6:07 PM, Vitaly Chaban vvcha...@gmail.com wrote: When I generate the tpr file with grompp, I

[gmx-users] Solvation free energy

file: free_energy = yes init_lambda = 0.00 sc_alpha= 0.5 sc_power= 1.0 sc_sigma= 0.3 What values do you suggest for these parameters? Thanks very much, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] mutation to/from proline

Hi, I want to calculate relative free energy associated to mutation of P1 (native protein) to p2 (mutated protein).In this mutation, Isolusine (in P1) is mutated to Proline(in P2). With using Thermodynamic cycle: Bilayer+P1= = = Bilayer-P1 delta G1

[gmx-users] Thickness

Hi, I used bilayer that consisted of 128 DOPC lipids as DOPC128.pdb as the primary bilayer and insert protein in bilayer with Inflategro program. when i expanded the bilayer, two DOPC molecules exited from box. i simulated this system and obtained the thickness of bilayer with GrigMAT_MD. i

[gmx-users] free energy

Hi, I inserted the protein in bilayer at Z normal and simulated membrane protein. to calculate free energy, it is better to use umbrella sampling tutorial from Justin Lemkul or free energy tutorial from David Mobley for my system? thanks, Afsaneh -- gmx-users mailing list

[gmx-users] Energy per residue

Dear gromacs users, Is there a way to get energy values (Vdw,..) per residue at the end of MD prosses? I would really appreciate any help. Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Energy per residue

Dear Justin, I want to get energy per residue not time. if i use mdrun -rerun with energygrps in md.mdp then g_energy i obtain enery per time not residue. at last, i don't understand how to get Energy per residue . Best wishes, Afsaneh afsaneh maleki wrote: Dear gromacs users

[gmx-users] order parameter for UAFF model

Hi all, i used united the atom force field model for the membrane lipids . to calculate order parameter i used : g_order -od -d i know united atom force field doesn't have hydrogen atoms in hydrocarbons chains . i want to know gromacs calculates order parameter * Sc-c* or *Sc-d*(Deuterium)

[gmx-users] Energy via residue

Hi all, How do i obtain the protein van der waals and electrostatic energies with bilayer via residue? highly appreciate!! Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] hblife

Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? thanks in advance, Afsaneh -- gmx-users mailing list

Re: [gmx-users] hblife

Best wishes, Afsaneh On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show

[gmx-users] The most probable secondary structure

Hi, how do i obtain the most probable secondary structure for each residue to analyze the detailed conformation of the peptide? i used do_dssp then converted *.eps to *.ps then obtained secondary structure. highly appreciate!! Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Density Profile

Hi, I obtained the electron density profile for the solvent in protein membrane simulation, For this I used the following commands: ]$ g_density -f md.xtc -s md.tpr -d z -dens electron -o sol.xvg -ei electrons.dat -symm -n index.ndx Although in md.gro file is seen any water in

[gmx-users] Electron Density

OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Electron Density2

Dear David van der Spoel, Would you please elaborate on the details? I didn’t underestand about “remove = sign” thanks in advans, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Electron Density3

Hi , I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains:

[gmx-users] order parameter for unsaturated chains

third term (sqr(3)/2 Syz) : but i don't know do i use this correlation for 8, 9 carbons or 9,10 ? because the segmental vector Cn-1 to Cn+1 is taken as the molecular axis of the Cn methylene group. thanks in advans, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] MSD

nm of protein. how can I obtain this index file thanks in advance, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

[gmx-users] grompp error in peptide-membrane simulations

) is in the dopc.itp and lipid.itp files but don't find in ffG43a2.rtp and .atp. i'm sure structure file is n't different in terms of the number of atoms , atomnames and the order of them with .itp files. any help will be hightly appreciated. -- Afsaneh Maleki PhD student of physical chemistry