[gmx-users] Question about Lysozyme in Water tutorial by Dr. Lemkul

suppose that negative Chlorine ions should be away from each other (same charge) and close to protein which has positive charge. which is not! is my simulation is incorrect? if not what cause this seemingly strange thing to happen? Thanks in advance for any guidance Best Regards, Nima Soltani

Re: [gmx-users] umbrella sampling tutorial

you must supply an index file to the '-n' option of grompp. Could anybody tell me what's wrong with the COM pulling code I modified? Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif

[gmx-users] Umbrella sampling Tutorial Fatal Error

, utilizing mgx make_ndx command at previous step Any advice or guidance would be greatly appreciated Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology

[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error

/gmxpreprocess/readpull.c, line: 257 Fatal error: Group pull_group1 required by grompp was undefined. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Best Regards, Nima Soltani

Re: [gmx-users] umbrella sampling - gromcas 5.0.4

-011-090-4495 Fax: +39-011-090-4499 E-mail: annalisa.cardellini@... SMaLL: http://www.polito.it/small Best Regards Nima Soltani Graduate student Sharif University of Technology -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] Installation problem

Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology. = -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] distance issues with umbrella sampling

-Nima Soltani Grad. student of physical chemistry Sharif Univ. of Tech. Dr Anthony Nash Department of Chemistry University College London -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Unusual Blow up

Justin Lemkul <jalemkul@...> writes: > > > On 9/1/15 9:40 AM, Nima Soltani wrote: > > Hi everyone > > I am simulating the interactions between a small peptide and different > > metallic surfaces solvated in TIP3P water. > > So far i have simulated 3

[gmx-users] Re : Unusual Blow up

Thank you for your kind help dear Justin this is link of one of the pdb files that has been generated after Blow up by Gromacs: https://www.dropbox.com/s/e3h05hohwp1va7p/step2170066b.pdb?dl=0 What other types of information do I need to provide? Best Regards, Nima Soltani

Re: [gmx-users] Unusual Blow up

Justin Lemkul <jalemkul@...> writes: > > > On 9/1/15 9:40 AM, Nima Soltani wrote: > > Hi everyone > > I am simulating the interactions between a small peptide and different > > metallic surfaces solvated in TIP3P water. > > So far i have simulated 3

Re: [gmx-users] Re : Unusual Blow up

Nima Soltani <nima.slt@...> writes: > > Thank you for your kind help dear Justin > this is link of one of the pdb files that has been generated after Blow up > by Gromacs: > https://www.dropbox.com/s/e3h05hohwp1va7p/step2170066b.pdb?dl=0 > What other types of informat

Re: [gmx-users] Re : Unusual Blow up

Nima Soltani <nima.slt@...> writes: > I really appreciate your time that you spend helping me Justin > the starting structure looks like this: > https://www.dropbox.com/l/qGSSN0MRJKUtJronECThnn > and the topology of the *metal* is: > https://www.dropbox.com/l/c0Cp7RUeua

Re: [gmx-users] Re : Unusual Blow up

Justin Lemkul <jalemkul@...> writes: > > > On 9/1/15 10:29 PM, Nima Soltani wrote: > > Nima Soltani ...> writes: > > > >> > >> Thank you for your kind help dear Justin > >> this is link of one of the pdb files that has been generated af

Re: [gmx-users] Re : Unusual Blow up

Justin Lemkul <jalemkul@...> writes: > > > On 9/2/15 11:59 AM, Nima Soltani wrote: > > Justin Lemkul ...> writes: > > > >> > >> > >> On 9/1/15 10:29 PM, Nima Soltani wrote: > >>> Nima Soltani ...> writes: > >>&g

[gmx-users] Unusual Blow up

--- Thanks in advance for any suggestions / assistance Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology

[gmx-users] anomalous eigenvector in PCA (Principal Component Analysis)

cture look likes this :https://app.box.com/s/e6b87ar9j75q227qe6sx1udeyqdszgdl ​Is there any way to correct those anomalies that can be observed in the peptide's backbone? thanks in advance for any help or guidance ​ Best Regards, Nima Soltani -

Re: [gmx-users] anomalous eigenvector in PCA (Principal Component Analysis)

Justin Lemkul <jalemkul@...> writes: > > > On 12/27/15 6:48 PM, Nima Soltani wrote: > > Hi > > I have performed principal component analysis by using g_covar module of > > Gromacs 5.0 (Peptide's backbone atoms were selected both for least square > >

[gmx-users] anomalous eigenvector in PCA (Principal Component Analysis)

cture look likes this : https://app.box.com/s/e6b87ar9j75q227qe6sx1udeyqdszgdl ​Is there any way to correct those artifices that can be observed in the peptide backbone? thanks in advance for any help or guidance ​ Best Regards, Nima Soltani -

[gmx-users] How to describe dynamic equilibrium between two states?

study adsorption kinetics from one simulation​? Millions of thanks in advance for any tips or guidance > > > Best Regards, > Nima Soltani > -- > MSc. of Physical Chemistry > Sharif University of Technology. > =====

[gmx-users] How to describe the Dynamic equilibrium between two states?

Hello dear GROMACS users I have recently submitted a manuscript ​ ​ ​about ​ ​ ​studying interactions of peptide-surface system. ​one of the referees has asked ​​ ​​ that : ​"​ "For the adsorption of the peptide on Au(111) in Figure 3 it seems that there is a dynamic equilibrium between two