[gmx-users] effect of slab geometry correction on Coulomb energies for interface systems

2011-06-08 Thread Ozge Engin
within the error bars even though I use different schemes for ewald_geometry? Regards -- Ozge Engin- PhD candidate Koc University, College of Engineering Dept. of Computational Sciences & Engineering Rumelifeneri

[gmx-users] problem with g_density

2010-10-25 Thread Ozge Engin
expect to get a number other than 0 at the lower and upper boundaries. I have also searched the mailing list. There was an e-mail similar to that one, but it was not replied. I have attached the density profile in the attachment. Why is it the case? Regards -- Ozge Engin dens.xvg Description

[gmx-users] error calculation via bootstrapping method in umbrella sampling simulation

2011-01-18 Thread Ozge Engin
depending on the block size used and number of bootstraps. I could not find a way to calculate the error for the umbrella sampling simulation by means of that output file. Thanks in advance -- Ozge Engin Department of

[gmx-users] "coarse_grain.tcl" script does not show all of the coarse-grained bonds in vmd

2009-12-03 Thread Ozge Engin
nds are created successfully, but when I looked at the screen I could see only one of those CG bonds, but not the others. Why might be the reason? Thanks in advance -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sear

[gmx-users] Re: gmx-users Digest, Vol 68, Issue 21

2009-12-03 Thread Ozge Engin
ns in topology file seem not working for big > systems (Berk Hess) > 3. "coarse_grain.tcl" script does not show all of the > coarse-grained bonds in vmd (Ozge Engin) > 4. Re: "coarse_grain.tcl" script does not show all of the > coarse-grained bon

[gmx-users] problem with the translate option of editconf

2010-02-15 Thread Ozge Engin
peptide is not translated, but sitting at the center of the box. Why is the case? Any suggestions? Thanks in advance -- Ozge Engin ★☆ -- 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

[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

2010-03-26 Thread Ozge Engin
hat may be the problem? Best Regards -- Ozge Engin ★☆ -- 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 requests to the list. Use

[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

2010-03-26 Thread Ozge Engin
+03 What may be the problem? Best Regards -- Ozge Engin ★☆ -- 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 requests to the list.

[gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water

2010-03-30 Thread Ozge Engin
problems. Kind Regards -- Ozge Engin ★☆ genera_start_4 Description: Binary data input Description: Binary data -- 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

[gmx-users] Re: gmx-users Digest, Vol 72, Issue 36

2010-04-08 Thread Ozge Engin
> The run ended successfully: > > > > > > > > > > > > Then i used the command > > > > > > g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr > > > > > > > > > > > > I get the follow

[gmx-users] Address for the server of a REMD temperature calculator

2008-01-31 Thread OZGE ENGIN
Hi all, Somebody has sent a mail which is about the address of a server in which the temperatures for a REMD simulation is calculated. However, I can not find this mail. Could you sent the address of the server, please? Thank you Ozge Engin = Computational

[gmx-users] exchanged pairs in the log file of a remd simulation

2008-02-03 Thread OZGE ENGIN
1.0 1.0 .70 .40 1.0 Replica exchange at step 47000 time 94 Line 2: Repl 2 <-> 3 dE = 7.473e-01 Repl ex 0 x 1234 x 56 x 78 x 9 10 11 12 13 Repl pr .04 .47 1.0 1.0 .65 .60 .34 Thanks in advanc

Re: Re: [gmx-users] exchanged pairs in the log file of a remd simulation

2008-02-03 Thread OZGE ENGIN
lman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin ===

[gmx-users] the 2 nd column of the output of g_cluster with -dist option

2008-02-12 Thread OZGE ENGIN
Hi all, What does the second column of the output file of g_cluster with -dist option stand for? Its title is a.u. I think it is atomic unit? In the manual, it is not described. Thanks in advance Ozge Engin = Computational Science & Engineering Koc Univer

Re: Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option

2008-02-12 Thread OZGE ENGIN
put of g_cluster with -dist option On Tue, 12 Feb 2008 23:55:35 +0200 "OZGE ENGIN" <[EMAIL PROTECTED]> wrote: > Hi all, > > What does the second column of the output file of g_cluster with -dist >option stand for? Its title is a.u. I think it is atomic unit? In the m

[gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix

2008-02-12 Thread OZGE ENGIN
rmsd matrix? Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] still got the problem with the output of g_cluster

2008-02-14 Thread OZGE ENGIN
the total number of conformations obtained from the simulation. Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs

Re: Re: [gmx-users] still got the problem with the output of g_cluster

2008-02-14 Thread OZGE ENGIN
Date: Fri, 15 Feb 2008 09:11:55 +1100 Subject: Re: [gmx-users] still got the problem with the output of g_cluster OZGE ENGIN wrote: > Hi all, > > I have still got the problem with the second column of the output of > g_cluster with -dist option. Xavier said that the a.u stands for arb

Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster

2008-02-14 Thread OZGE ENGIN
s the sum of the second column? Mark - Original Message - From: OZGE ENGIN <[EMAIL PROTECTED]> Date: Friday, February 15, 2008 9:46 am Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster To: gmx-users@gromacs.org > Hi Mark, > > You are right

Re: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster

2008-02-15 Thread OZGE ENGIN
i.e. 3001*3000*0.5, which is the number you give below. The values in this column are consistent with a histogram. Mark - Original Message ----- From: OZGE ENGIN <[EMAIL PROTECTED]> Date: Friday, February 15, 2008 6:32 pm Subject: Re: Re: Re: [gmx-users] still got the problem wi

[gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual

2008-02-15 Thread OZGE ENGIN
RMS deviation. What is the difference between these two? One of them gives the absolute rmsd of each frame and the other gives the relative rmsd according to the average rmsd? Thanks in advance Ozge Engin = Computational Science & Engineering Koc Univer

[gmx-users] "rmsd distance" and "rmsd deviation" option for the -dista option of g_cluster

2008-02-15 Thread OZGE ENGIN
Hi all, There are two options for the -dista option of the g_cluster: rmsd of distance and RMS deviation. What is the difference between these two? One of them gives the absolute rmsd of each frame and the other gives the relative rmsd according to the average rmsd? Thank you Ozge Engin

Re: [gmx-users] Stanford workshop april 7-8

2008-02-16 Thread OZGE ENGIN
D] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/l

[gmx-users] distance options for g_cluster

2008-02-16 Thread OZGE ENGIN
t;other options" part for -dista option. Maybe I could not understand. Could anyone explain this in a clearer way, please? Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ g

Re: Re: [gmx-users] distance options for g_cluster

2008-02-17 Thread OZGE ENGIN
me cut-off value, they are grouped in different clusters, Why? Thank you. -Original Message- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 17 Feb 2008 22:35:20 +1100 Subject: Re: [gmx-users] distance options for g_cluster OZGE ENGIN wrote:

[gmx-users] which type of cysteine residue?

2008-02-23 Thread OZGE ENGIN
parameters for dihedral angles. Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please se

[gmx-users] problem with exchange probabilities in remd

2008-02-23 Thread OZGE ENGIN
nks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: Re: [gmx-users] problem with exchange probabilities in remd

2008-02-24 Thread OZGE ENGIN
roblem with exchange probabilities in remd OZGE ENGIN wrote: > Hi all, > > I am performing a remd simulation of a peptide+water system. I have tried > different temperature distributions. I am using an NVT ensemble. My > temperature coupling constant is 0.1 ps. > > The proble

[gmx-users] procedure for creating an S-S bridge

2008-03-02 Thread OZGE ENGIN
bond. What additional steps do I follow to construct this bond ? Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs

Re: Re: [gmx-users] procedure for creating an S-S bridge

2008-03-03 Thread OZGE ENGIN
ers@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can&#x

Re: Re: Re: [gmx-users] procedure for creating an S-S bridge

2008-03-03 Thread OZGE ENGIN
chive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computationa

[gmx-users] incorporation of distance restraint into the topology file

2008-03-03 Thread OZGE ENGIN
numbers into these columns. P.S: I use Gromacs 3.3.1 Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

[gmx-users] pbc on the "xy" direction

2008-03-10 Thread OZGE ENGIN
ot; and "no") . How can I implement it to my system? I use Gromacs 3.3.1 version. Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@

[gmx-users] changing the time step with tpbconv

2008-03-21 Thread OZGE ENGIN
the main (longer) simulation. Consequently, I want to change the time step and use tpbconv to restart. Is there any way to do that? Thanks in advance... Ozge Engin = Computational Science & Engineering Koc Univer

Re: Re: [gmx-users] changing the time step with tpbconv

2008-03-21 Thread OZGE ENGIN
ubject: Re: [gmx-users] changing the time step with tpbconv OZGE ENGIN wrote: > Hi all, > > I am performing an 80-ns simulation. During the optimization of the > parameters that were used in this run, I had performed some small test > simulations, and used short frequency values to

[gmx-users] problem with grompp (that is used instead of tpbconv)

2008-03-21 Thread OZGE ENGIN
, VERSION 3.3.1 Source code file: grompp.c, line: 542 Fatal error: Can not start from an incomplete frame Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs

[gmx-users] transfer of AMBER ion definitions to the ions.itp file

2008-03-29 Thread OZGE ENGIN
that, I will copy the ions definitions that were given in the ffamber96.rtp file to the ions.itp file? I am a little bit confused because the definition of ions in AMBER is completely different from those of OPLS and GROMOS ff. Thanks in advance Ozge Engin

Re: Re: [gmx-users] transfer of AMBER ion definitions to the ions.itp file

2008-03-29 Thread OZGE ENGIN
9 Mar 2008 11:54:22 -0400 Subject: Re: [gmx-users] transfer of AMBER ion definitions to the ions.itp file Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I am trying to use AMBER96 ff under GROMACS package. I read the suggestions > that were given at http://chemistry.csulb.

[gmx-users] residue names for AMBER ff in GROMACS

2008-03-30 Thread OZGE ENGIN
corresponding H names of this residue have been defined in .rtp and .hdb,respectively. So, what may be the problem? Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-u

[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

2008-03-31 Thread OZGE ENGIN
+++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? Thanks in advance Ozge Engin = Computational Science & Engineering Koc Univer

Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

2008-03-31 Thread OZGE ENGIN
ce for the force on atoms. -Original Message- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN <[EMAIL PRO

Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

2008-03-31 Thread OZGE ENGIN
or GROMACS users Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > I already indicated the problem that I have. If I put an N prefix to the > first residue, I get warning of

Re: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

2008-03-31 Thread OZGE ENGIN
again. -Original Message- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 31 Mar 2008 17:41:50 -0400 Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN <[EMAIL PROTECTED]

[gmx-users] g_sas to calculate the n-hexane/water interface surface area

2010-04-13 Thread Ozge Engin
should give me that area? Regards -- Ozge Engin ★☆ -- 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 requests to the list. Use the w

[gmx-users] g_sas command with the -q option

2010-04-15 Thread Ozge Engin
calculation? Regards -- Ozge Engin ★☆ -- 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 requests to the list. Use the www interface or

[gmx-users] number of water molecules affects the PMF

2010-06-01 Thread Ozge Engin
sets. I searched the internet to find a study regarding the concentration dependency of the PMF. Is this reasonable? Any suggestions? Regards Ozge Engin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 13

2010-06-01 Thread Ozge Engin
-af3d-e6c88393d...@rug.nl> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote: > > > Hi all, > > > > I am trying to calculate the potential of mean force between the two > > hydr

[gmx-users] number of water molecules affects the PMF

2010-06-02 Thread Ozge Engin
the whole data to 4, and calculated the standard deviation between the 4 sets, and divided the result by sqrt (3). For the Xavier's suggestion: I think I should wait a little, at least until having the same length of trajectory for the two sets. Thanks -- Ozge Engin ★☆ -- gmx-users mailing

[gmx-users] output of the -hist option of the g_wham command

2010-06-22 Thread Ozge Engin
what does "histogram of configurations" mean? Thank you -- Ozge Engin ★☆ -- 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] information regarding the bootstrap method implemented with the g_wham

2010-07-09 Thread Ozge Engin
little bit detailed information, please? Thanks in advance -- Ozge Engin ★☆ -- 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 req

[gmx-users] Different hexane/water surface tensions fo r different ensembles (NVT and NAɣT)

2010-08-24 Thread Ozge Engin
straightforward? Regards -- Ozge Engin ★☆ -- 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 requests to the list. Use the www inte

[gmx-users] problem with genion

2007-05-17 Thread OZGE ENGIN
: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype CU1+ is redefined What is the problem? Thanks in advance Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo

[gmx-users] problem with position-restrained dynamics of a charged system

2007-05-22 Thread OZGE ENGIN
, what may be the problem? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

Re: Re: [gmx-users] problem with position-restrained dynamics of a charged system

2007-05-22 Thread OZGE ENGIN
rotein 1 NA+ 12 SOL 1589 OZGE ENGIN a écrit : > Hi all, > > I have a problem with position-restrained (pr) dynamics of a charged residue > in a water box. Up to the position-restrained step, the method worked well; > however, it gave the f

Re: Re: [gmx-users] problem with position-restrained dynamics of a charged system

2007-05-22 Thread OZGE ENGIN
rotein 1 NA+ 12 SOL 1589 OZGE ENGIN a écrit : > Hi all, > > I have a problem with position-restrained (pr) dynamics of a charged residue > in a water box. Up to the position-restrained step, the method worked well; > however, it gave the f

Re: Re: [gmx-users] problem with position-restrained dynamics of a charged system

2007-05-22 Thread OZGE ENGIN
rained dynamics of a charged system Maybe you have forget to include something (I don't know exactly what) ... is it possible to post your top and gro files (attached and zipped) ? it will be easier to find what happened :P . OZGE ENGIN a écrit : > Yes, Sebastien! It ends as you wrote. So, it

Re: Re: [gmx-users] problem with position-restrained dynamics of a charged system

2007-05-22 Thread OZGE ENGIN
rained dynamics of a charged system Maybe you have forget to include something (I don't know exactly what) ... is it possible to post your top and gro files (attached and zipped) ? it will be easier to find what happened :P . OZGE ENGIN a écrit : > Yes, Sebastien! It ends as you wrote. So, it

[gmx-users] problem with the output file of g_density

2007-06-04 Thread OZGE ENGIN
Dear gromacs-users, I have a problem with the output file of g_density. It uses .tpr and .trr files in order to make calculations. I have made the .trr file using the parameters below. Since total step size is 100 and I have written the coordinates at each 50 steps, I expect to have more th

[gmx-users] adding counter ions

2007-06-08 Thread OZGE ENGIN
the system? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subs

Re: Re: [gmx-users] adding counter ions

2007-06-12 Thread OZGE ENGIN
tween the oppositely charged residues :-) is not far apart than the optimum which means that they are located at such a distance that they have the ability to cancel each other. Thank you... Ozge Engin -Original Message- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussi

[gmx-users] Problem with g_rdf /option com

2007-06-19 Thread OZGE ENGIN
Hi, I want to get the radial distribution of my system which is composed of a box of capped alanine residues (CAR). In this respect, I used g_rdf command with -com option. I chose one of the CAR s as the first, and the others as the second group. In manual, for -com option, it is written that t

[gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem

2007-08-24 Thread OZGE ENGIN
Hi gromacs-users, I want to simulate a box of that is composed of capped (ACE and NME to N and C termini, respectively) tryptophan molecules. As a first stage, I minimized single capped trp molecule, and then used it with genconf command along with the options -rot ans -nbox. In this case, I

[gmx-users] Minimization of a box of capped tryptophan (trp)

2007-08-25 Thread OZGE ENGIN
Hi all, As you suggest David I used genconf command without -rot option. I minimized a single capped trp molecule and got the minimized molecule and used that molecule with genconf command in order to create a box. > > Then, I solvated capped trp molecule within the created box with genbox > c

[gmx-users] Appropriate command for measuring density of the whole simulation box along the trajectory

2007-08-28 Thread OZGE ENGIN
Hi all, I want to measure the density or volume of the whole simulation box not only the molecule. I could not find an appropriate command. I found some;however, they measured the partial densities across the box. Thanks in advance... Ozge ___ gmx-u

[gmx-users] r_list and r_coulomb values while using PME

2007-09-01 Thread OZGE ENGIN
Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advanc

Re: Re: [gmx-users] r_list and r_coulomb values while using PME

2007-09-01 Thread OZGE ENGIN
ntion! Oz. -Original Message- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sat, 01 Sep 2007 13:37:05 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: > Hi all, > > I can not underst

Re: Re: [gmx-users] r_list and r_coulomb values while using PME

2007-09-01 Thread OZGE ENGIN
ubject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: > 'The force is not the derivative of the potential', is it due to the types of > calculations performed in PME, using of FFT for reciprocal sum? Because it > does not matter while using reacti

[gmx-users] Charge of CH2r atoms in Gromos 53A6 force-field

2007-09-04 Thread OZGE ENGIN
Hi all, I have read the manual of Gromos force field with parameter set 53A6. I am trying to get the topology file of cyclohexane molecule. In a paper which defined the parameters of Gromos 53A5 and 53A6 force-fields, it is said that atoms that are not listed have a zero charge, and the charge

[gmx-users] Tool for visualizing disulphide bonds

2007-10-14 Thread OZGE ENGIN
Hi all, Is there any tool for the visualization of disulphide bonds along the whole trajectory? Regards, Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

Re: Re: [gmx-users] the comm_mode

2007-10-14 Thread OZGE ENGIN
Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? Thanks in advance Ozge -Original

Re: Re: Re: [gmx-users] the comm_mode

2007-10-14 Thread OZGE ENGIN
visible. Is it related to conservation of angular momentum? Thank you very much! Oz. -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT) Subject: Re: Re: [gmx-users] the comm_mode - Original Message Fro

[gmx-users] Addition of ions in vacuum simulations

2007-10-17 Thread OZGE ENGIN
Hi all, I am simulating a charged peptide in vacuum. I want to neutralize my system by using genion command,and as expected it asks me a continuous solvent group for the replacement; however, I have no solvents. How can I add ions to my system if I am in vacuum? or Is it necessary to add ions

Re: Re: [gmx-users] Addition of ions in vacuum simulations

2007-10-18 Thread OZGE ENGIN
Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? Thanks Ozge -Original Message- From: "Mark Abraham" <[EM

[gmx-users] Placing a peptide at the air/water interface

2007-11-04 Thread OZGE ENGIN
Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in o

[gmx-users] Placing a peptide at the air/water interface

2007-11-04 Thread OZGE ENGIN
Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in o

Re: [gmx-users] Placing a peptide at the air/water interface

2007-11-04 Thread OZGE ENGIN
Hi Mark, I am so sorry, but I erased your mail before reading it. So, could you please send the mail one more time? It is important to me. Thank you very much Ozge -Original Message- From: "OZGE ENGIN" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Sun, 04 Nov 200

[gmx-users] Performing simulation at air/water interface

2007-11-05 Thread OZGE ENGIN
Hi all, I am performing a simulation of peptide at air/water interface. The box vectors are: x,y,z where 2x=2y=z. After loading the trajectory to the vmd, I realized that water molecules moved out of bulk water in the z direction: into the vacuum. However, the peptide also moved out of the bulk

Re: Re: [gmx-users] Performing simulation at air/water interface

2007-11-05 Thread OZGE ENGIN
rforming simulation at air/water interface Regarding the peptide moving out of the box, it is only a visualization artifact. Try trjconv -pbc inbox. 2007/11/5, OZGE ENGIN <[EMAIL PROTECTED]>: > > Hi all, > > I am performing a simulation of peptide at air/water interface. > &g

[gmx-users] (no subject)

2007-11-09 Thread OZGE ENGIN
I want to use replica exchange method. After obtaining all files at different temperatures, how can I load the e.g 4 separate replica files to the mdrun command? I could not find any information about it. Thank you Oz. ___ gmx-users mailing listg

[gmx-users] trjconv does not work!

2007-11-19 Thread OZGE ENGIN
Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) W

[gmx-users] trjconv does not work

2007-11-19 Thread OZGE ENGIN
Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) W

Re: Re: [gmx-users] trjconv does not work

2007-11-19 Thread OZGE ENGIN
t work Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: > Hi all, > > I want to extract some frames from the whole trajectory. So, I used -trjconv > with (b) and (e) options. > > P.S: I use the Gromacs 3.3.1 version. > > But I got the following error: &g

Re: Re: [gmx-users] trjconv does not work

2007-11-19 Thread OZGE ENGIN
t work Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: > Hi all, > > I want to extract some frames from the whole trajectory. So, I used -trjconv > with (b) and (e) options. > > P.S: I use the Gromacs 3.3.1 version. > > But I got the following error: &g

Re: Re: [gmx-users] trjconv does not work

2007-11-19 Thread OZGE ENGIN
n list for GROMACS users Date: Mon, 19 Nov 2007 17:53:16 +0100 Subject: Re: [gmx-users] trjconv does not work I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: > The command line ws the following: > > trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -

Re: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

2007-11-23 Thread OZGE ENGIN
option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: Re: RE: [gmx-

[gmx-users] problem with mdrun performing replica exchange MD

2007-11-23 Thread OZGE ENGIN
Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error:

Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

2007-11-23 Thread OZGE ENGIN
t; To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-

Re: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD

2007-11-23 Thread OZGE ENGIN
e the CVS head branch, you need to set -np and -multi both with an argument. Berk. >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: Re: RE: [gmx-users] problem with mdrun performing replica exch

[gmx-users] Neutralizing the total charge of the system in vacuum

2007-11-24 Thread OZGE ENGIN
Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total ch

[gmx-users] Problem with replica exchange in vacuum

2007-11-25 Thread OZGE ENGIN
Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. Although I started to the simulation vi

[gmx-users] Problem with replica exchange in vacuum

2007-11-25 Thread OZGE ENGIN
Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. Although I started to the simulation vi

[gmx-users] The fifth column of the output file of g_sas command

2007-11-27 Thread OZGE ENGIN
Hi all, I have a question about the output file of g_sas. The fifth column corresponds to Solvation free energy. I selected the whole peptide for analyzing. It did not take negative value, but rather it took positive values. As it takes larger + values, it means that the peptide or group under

Re: [gmx-users] Replica Exchange MD using Gromacs

2007-11-30 Thread OZGE ENGIN
Hi Monica, I had not found a detailed tutorial about it; however, you can search for papers in which the simulations are performed via REMD.This will be helpful. Ozge. -Original Message- From: "Monika Sharma" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Fri, 30 Nov 2007 17:04:07

[gmx-users] g_hbond

2006-12-18 Thread OZGE ENGIN
Hi, I have a problem with g_hbond. I want to investigate the H bonds formed not only within the protein but also between water molecules and the protein.In this respect, I select the group 0 --> 'system' option for both selections, an error message like the following one appears: Segmentation

Re: Re: [gmx-users] g_hbond

2006-12-18 Thread OZGE ENGIN
Message- From: Erik Marklund <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Mon, 18 Dec 2006 13:48:18 +0100 Subject: Re: [gmx-users] g_hbond On Mon, 2006-12-18 at 13:34 +0200, OZGE ENGIN wrote: > Hi, > > I have a problem with g_hbond. I want to investigate the

[gmx-users] g_hbond in/output

2006-12-20 Thread OZGE ENGIN
Hi, I have some questions about g_hbond option. 1) My system consists of a protein molecule (a capped 1 alanine residue) (CH3-CO-ALA-NH-CH3) and 250 water molecules. After selecting the g_hbond option, it says that protein molecule consists of 12 elements; however, it consists much more el

[gmx-users] -sel option / g_hbond

2006-12-26 Thread OZGE ENGIN
Hi, First of all, thank you very much for your earlier explanations, they helped me much. Now, I have a problem with the -sel option of g_hbond. I want to analyze the specific hydrogen bonds in my system, in this respect I created a file (.ndx), and then I called it with the -sel option. The

[gmx-users] ghbond/- hbn option

2007-01-02 Thread OZGE ENGIN
Hi, I have a problem with the -hbn option. I could not understand the output given. It is indicated that there is only one type of hydrogen bond is formed between the donor and acceptor (Only one triplet is given). It means that the same hydrogen bond is formed between the same atoms during th

[gmx-users] /x?.FPIB.CCI_6NF.QSgKkRQ.a

2007-01-09 Thread OZGE ENGIN
Hi, By using the hnum option of g_hbond, I was able to get the hbond.ndx file. However, I want to know exactly which atom groups take participate to the formation of that hbonds over each frame both for prot-prot and prot-solvent. How can I do that? (In hbond.ndx file, as you know, the hbonds

[gmx-users] hbond types over each frame

2007-01-09 Thread OZGE ENGIN
Hi, By using the hnum option of g_hbond, I was able to get the hbond.ndx file. However, I want to know exactly which atom groups take participate to the formation of that hbonds over each frame both for prot-prot and prot-solvent. How can I do that? (In hbond.ndx file, as you know, the hbonds a

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