@ Vivek,
You are separating after 3.5 months of employment. You have posted the reason as "the work environment is also not favorable for growth." Kindly allow to reiterate that employee should also carefully find out about the company from experienced peers, colleagues, consultants, web sites and join after satisfaction. The candidates/employees who move methodically and consult before hand, seldom face inconvenience, teething problems, loss.
While in your case you are eligible to separate but how would you justify your tenure of 3.5 months to recruiters in future.
Any company good or bad would not like to be treated as hoping/training ground and take their efforts to recruit and train for a ride.
This could be the reason of approach of HR in your case.
The conditions expressed in your appointment letter as posted by you are not sever or harsh.
You may quote the termination clause and mention in writing by letter (followed by email) addressed to good offices of your appointing authority, Head-HR, MD, that subsequent to your notice of resignation dated........... With effective date of resignation as dated.......you are willing to tender notice pay for the shortfall in notice period for .........days @ basic salary as described in your appointment letter at clause number..........and company should inform you in writing that this notice pay shall be adjusted in FNF statement. The acknowledgment of your notice of resignation may be supplied to you immediately and acceptance of resignation, settlement of your dues, FNF payment, FNF amount by bank DD, work experience/service certificate, relieving letter, form 16, PF number and PF accumulation report, PF withdrawal/transfer form, NDC/NOC should be supplied to you by hand within your last working day, and charge should be taken from you under acknowledgment.
You may enclose a list of dues at your end e.g company property, advance/imprested cash if any and list of dues/payables by company to you and request the good offices to check and confirm the same and let you know for the variances if any to avoid any los of time, funds at the end of both the parties.
You may mention during this one month period you are willing to train the designated employee and company should inform you well in time about this and to whom company property should be submitted under acknowledgment.
If you are willing to do so you can enclose the cheque for notice pay of 1 month @ basic pay along with your letter and mention the cheque number in your letter.